Search results for query "look through"

527 messages

Re: [cctbxbb] some thoughts on cctbx and pip

by Gergely Katona

Dear Billy, Thank you for this update and for your efforts! I found a solution and indeed most things already work in anaconda3. The steps I took (even if these instructions will have short expiry date): Modified .condarc with: channels: - cctbx - conda-forge - defaults run conda conda install cctbx_dependencies python=3.6 I expect this will work without python=3.6 in the near future. Then compiling cctbx with anaconda3 python went without any problem when using these flags: python bootstrap.py --use-conda --python3 --nproc=12 Then I probably did the unorthodox thing and sourced these directories: setenv LIBTBX_BUILD /home/gergely/cctbx/build setenv PATH ${PATH}:/home/gergely/cctbx/build/bin setenv PYTHONPATH /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH setenv LD_LIBRARY_PATH /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH There is probably a better way to put this into conda environment. With these steps I could run one of my scripts depending on cctbx. The only problem I found is that hdf5 library had conflict with another package in conda, but I does not find this as a showstopper. Best wishes, Gergely On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > > Hi Gergely, > > It's still a work in progress. I'm sorting out some Windows issues right now. I can probably build a test package on a separate channel for people that want to test it (let's say next week?). I'll provide instructions, but basically, the test conda package will be in its own separate channel and the dependencies will be pulled from the conda-forge channel. I want most things to be working correctly on Python 2.7, 3.6, 3.7, and 3.8 on all 3 platforms. > > Thanks! > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <gkatona(a)gmail.com> wrote: >> >> Dear Billy, >> >> This sounds very promising and exciting. I am not sure if cctbx is >> already functional as a conda package in anaconda3 (Linux) or this is >> still work in progress. My technical expertise does not allow me to >> tell the difference. What I tried: >> >> Fresh install of anaconda3. Adding - cctbx and - conda-forge to >> .condarc . Installing pyside2 with conda. Running conda install >> conda_dependencies . I get a lot package version conflict, and I >> cannot import cctbx or iotbx to anaconda python. Am I following the >> right instructions? Or it is too early to expect that cctbx works when >> installed through conda? >> >> Best wishes, >> >> Gergely >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> wrote: >> > >> > Hi all, >> > >> > For a brief update, I have submitted a recipe for cctbxlite to conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021) and support for Python 3.7 and 3.8 is being added (https://github.com/cctbx/cctbx_project/pull/409). With some fixes for Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. Some additional changes will be needed to get Windows to work with Python 3 and for tests to pass with Boost 1.70.0. That will enable the conda-forge recipe to build for all platforms and for all supported versions of Python. >> > >> > Currently, the conda-forge recipe will install into the conda python and cctbx imports can be done without sourcing the environment scripts. It looks like a lot of the environment variables being set in the dispatchers can be removed since the Python files and C++ extensions are in the right places. I'll update the libtbx_env file so that commands that load the environment can work correctly. >> > >> > -- >> > Billy K. Poon >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> > Lawrence Berkeley National Laboratory >> > 1 Cyclotron Road, M/S 33R0345 >> > Berkeley, CA 94720 >> > Tel: (510) 486-5709 >> > Fax: (510) 486-5909 >> > Web: https://phenix-online.org >> > >> > >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> wrote: >> >> >> >> Hi Luc, >> >> >> >> That sounds promising. From there, I’d need to work out how to make a fully-packaged installer (basically a modified wheel file) for the ChimeraX ToolShed - the aim is for the end user to not have to worry about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD would need to be set dynamically before first import - but doesn’t seem insurmountable. >> >> >> >> Thanks, >> >> >> >> Tristan >> >> >> >> >> >> >> >> Tristan Croll >> >> Research Fellow >> >> Cambridge Institute for Medical Research >> >> University of Cambridge CB2 0XY >> >> >> >> >> >> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: >> >> > >> >> > Hi Tristan, >> >> > >> >> > cctbx could be built to use your ChimeraX python, now that cctbx is moving to Python 3. The option —with-python is there for that with the bootstrap script. The specific environment setup boil down to setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a framework such as ChimeraX, that should not be difficult to ensure those two variables are set. >> >> > >> >> > Best wishes, >> >> > >> >> > Luc >> >> > >> >> > >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> wrote: >> >> >> >> >> >> To add my two cents on this: probably the second-most common question I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The honest answer to that is, "I didn't know how." >> >> >> >> >> >> Still don't, really - although the current developments are rather promising. The problem I've faced is that CCTBX was designed as its own self-contained Python (2.7, until very recently) environment, with its own interpreter and a lot of very specific environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained Python (3.7) environment. To plug one into the other in that form... well, I don't think I'm a good enough programmer to really know where to start. >> >> >> >> >> >> The move to Conda and a more modular CCTBX architecture should make a lot more possible in that direction. Pip would be even better for me personally (ChimeraX can install directly from the PyPI, but doesn't interact with Conda) - but I understand pretty well the substantial challenge that would amount to (not least being that the PyPI imposes a limit - around 100MB from memory? - on the size of an individual package). >> >> >> >> >> >> Best regards, >> >> >> >> >> >> Tristan >> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: >> >> >>> Hi Graeme, >> >> >>> Yes, I know. But “black" is a program doing a very particular task >> >> >>> (code formatting from the top of my head). Requiring to use a wrapper >> >> >>> for python itself is another level. But ok, I think I am mellowing to >> >> >>> the idea after all! Talking with people around me, and extrapolating, >> >> >>> I would bet that, right now, a great majority of people interested by >> >> >>> cctbx in pip have already used the cctbx, so they know about the >> >> >>> Python wrapper, and they would not be too sanguine about that. My >> >> >>> concern is for the future, when pip will be the first time some people >> >> >>> use cctbx. Big fat warning notices on PyPI page and a better error >> >> >>> message when cctbx fails because LIBTBX_BUILD is not set would be >> >> >>> needed but that could be all right. >> >> >>> If we do a pip installer, we should aim at a minimal install: cctbx, >> >> >>> iotbx and their dependencies, and that’s it. >> >> >>> Best wishes, >> >> >>> Luc >> >> >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: >> >> >>>> Without discussing the merits of this or whether we _choose_ to make the move to supporting PIP, I am certain it would be _possible_ - many other packages make dispatcher scripts when you pip install them e.g. >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) >> >> >>>> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >> >> >>>> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >> >> >>>> # -*- coding: utf-8 -*- >> >> >>>> import re >> >> >>>> import sys >> >> >>>> from black import main >> >> >>>> if __name__ == '__main__': >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) >> >> >>>> sys.exit(main()) >> >> >>>> So we _could_ work around the absence of LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is a different question, and it seems clear that here are very mixed opinions on this. >> >> >>>> Best wishes Graeme >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >>>> Hi, >> >> >>>> Even if we managed to ship our the boost dynamic libraries with pip, it would still not be pip-like, as we would still need our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages work with the standard python exe. LD_LIBRARY_PATH, we could get around that by changing the way we compile, using -Wl,-R, which is the runtime equivalent of build time -L. That’s a significant change that would need to be tested. But there is no way around setting LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps there is a way to hack libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip installs? >> >> >>>> Best wishes, >> >> >>>> Luc >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >>>> Hi, >> >> >>>> I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. >> >> >>>> Best wishes, >> >> >>>> Luc >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >> >> >>>> Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. >> >> >>>> All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. >> >> >>>> There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). >> >> >>>> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. >> >> >>>> Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) >> >> >>>> Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. >> >> >>>> Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. >> >> >>>> Thanks, >> >> >>>> -Aaron >> >> >>>> _______________________________________________ >> >> >>>> cctbxbb mailing list >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >>>> _______________________________________________ >> >> >>>> cctbxbb mailing list >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >>>> _______________________________________________ >> >> >>>> cctbxbb mailing list >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >>>> -- >> >> >>>> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. >> >> >>>> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. >> >> >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. >> >> >>>> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >>>> _______________________________________________ >> >> >>>> cctbxbb mailing list >> >> >>>> cctbxbb(a)phenix-online.org >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >>> _______________________________________________ >> >> >>> cctbxbb mailing list >> >> >>> cctbxbb(a)phenix-online.org >> >> >>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> cctbxbb mailing list >> >> >> cctbxbb(a)phenix-online.org >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> > >> >> > >> >> > _______________________________________________ >> >> > cctbxbb mailing list >> >> > cctbxbb(a)phenix-online.org >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> _______________________________________________ >> >> cctbxbb mailing list >> >> cctbxbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> > >> > _______________________________________________ >> > cctbxbb mailing list >> > cctbxbb(a)phenix-online.org >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> -- >> Gergely Katona, PhD >> Associate Professor >> Department of Chemistry and Molecular Biology, University of Gothenburg >> Box 462, 40530 Göteborg, Sweden >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb -- Gergely Katona, PhD Associate Professor Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 Web: http://katonalab.eu, Email: gergely.katona(a)gu.se

6 years, 1 month

Re: [phenixbb] help with phenix.ligand_identification

by Li-Wei Hung

Hi Ed, Sorry for problems in ligand_identification. The default is to use LigandFit processes (slower, but more thorough), so the search center syntax will be under ligandfit.search_target.search_center. You can on the other hand use the faster ligand_id process with use_ligandfit=False, the your search_center should work. I noticed that you are using map coefficients so mtz_type=diffmap should be set. I short, you can either phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" mtz_type=diffmap\ model=sqr2803or13_031.pdb ligandfit.search_target.ligand_near_chain=S ligandfit.search_target.ligand_near_res=2063 nproc=2 .... (the two ligandfit.search_targets.ligand_near_xxx, and be replaced by ligandfit.search_target.search_center="n.n n.n n.n") or phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" mtz_type=diffmap\ model=sqr2803or13_031.pdb use_ligandfit=false ligand_near_res="chain S and resid 2063" (or search_center="n.n n.n n.n" )nproc=2 If you have further problems or questions on ligand_identification, please do not hesitates to email me with input files (off list), and I'll help straighten problems. In any event, I will update the documentation to add examples, and probably change one of the search_center keywords to make things clearer. Best regards, Li-Wei Edward A. Berry wrote: > Ligandfit itself has more helpful error message: > Sorry the string 'S2063' cannot be interpreted as a residue number? > (Duh!) > and does actually place the ligand in the requested blob with > "search_center=" > So I can run ligandfit in a foreach loop with each of the 180 ligands > left by ligand_identification > ================= > > On 09/26/2017 03:32 PM, Edward A. Berry wrote: >> I'm having some problems using ligand_identification. >> I would like to restrict the search to a specific density peak, even >> if it is not the highest unmodeled peak or the highest Fo-Fc peak in >> the map. >> I tried using options: >> search_center="67.5 18.3 11.8" >> or >> ligand_near_res=S2063, >> Will the search be restricted to that region, or if a particuar >> ligand doesn't fit that blob, >> will it search through the rest of the map? If it is restricted, in >> what radius? >> Is this radius affected by the "search_dist" or "local_search" >> parameters? >> and local_search = True is default? >> Is there a threshold level for density level, below which building a >> ligand in a blob will not be attempted? >> >> I've tried with both search_center= and ligand_near_res=, and >> something gets >> built far away from that site. But there were errors, so I may have >> something wrong: >> >> >> phenix.ligand_identification mtz_in=sqr2803or13_031.mtz >> input_labels="2FOFCWT PH2FOFCWT" \ >> model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2 >> >> After preparing the ligand library, then: >> Running LigandFit process 1... >> >> Number of atoms in ligand suc.pdb is 23 >> Running job sequence 1, ligand 2, in >> /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1... >> Evaluating all ligands in ligand-lib now...and placing fittedligand >> ### in resolve_ligand_###.pdb >> >> Number of atoms in ligand 2pe.pdb is 28 >> Running job sequence 0, ligand 1, in >> /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0... >> Process Process-2: >> Traceback (most recent call last): >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 258, in _bootstrap >> self.run() >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 114, in run >> self._target(*self._args, **self._kwargs) >> File >> "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", >> line 1382, in RunLigandFit >> shutil.rmtree(ligandfit_dir) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 247, in rmtree >> rmtree(fullname, ignore_errors, onerror) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 256, in rmtree >> onerror(os.rmdir, path, sys.exc_info()) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 254, in rmtree >> os.rmdir(path) >> OSError: [Errno 39] Directory not empty: >> '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0' >> Process Process-1: >> Traceback (most recent call last): >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 258, in _bootstrap >> self.run() >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 114, in run >> self._target(*self._args, **self._kwargs) >> File >> "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", >> line 1382, in RunLigandFit >> shutil.rmtree(ligandfit_dir) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 247, in rmtree >> rmtree(fullname, ignore_errors, onerror) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 256, in rmtree >> onerror(os.rmdir, path, sys.exc_info()) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 254, in rmtree >> os.rmdir(path) >> OSError: [Errno 39] Directory not empty: >> '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0' >> >> Evaluating LigandFit results ... >> >> The run continues, but it does not test any more ligands after those >> first two but goes on to evaluate the results. >> With nproc = 1, only 1 ligand gets tested. In all cases the first >> ligand in the library (2PE.pdb) is evaluated as the best. >> It is placed in density, but density that has already been built out >> with (and looks more like) a string of water molecules. >> And this is far from the selected residue or coordinates specified. >> >> The directory that raised the error when attempting to be deleted >> does eventually get removed: after the run there is no TEMP_N in the >> parent directory. >> >> Any suggestions would be welcome. >> Ed >> >> P.S. >> - running with .eff file: >> >> >> ['--show_defaults'] >> ligand_identification { >> mtz_in = sqr2803or13_031.mtz >> mtz_type = *F diffmap >> model = sqr2803or13_031.pdb >> ncpu = 1 >> n_indiv_tries_min = 30 >> n_indiv_tries_max = 300 >> n_group_search = 4 >> search_dist = 10 >> local_search = True >> search_center = "67.5 18.3 11.8" >> # ligand_near_res = S2063 >> verbose = False >> debug = False >> use_ligandfit = True >> search_mode = *default LigandFit >> temp_dir = Auto >> dry_run = False >> # number_of_ligands = 1 >> cc_min = 0.75 >> open_in_coot = False >> non_bonded = True >> keep_all_files = False >> # cif_def_file_list = >> real_space_target_weight = 10 >> # job_title = None >> ligandfit { >> } >> } >> >> gives: >> >> [['2pe.pdb', 'suc.pdb', . . . 'upl.pdb']] >> >> /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2 >> >> ******************************************************************************* >> >> >> Sorry, the protein model file None does not seem to exist? >> >> ******************************************************************************* >> >> >> >> Running LigandFit process 0... >> >> Process Process-1: >> Traceback (most recent call last): >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 258, in _bootstrap >> self.run() >> File >> "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", >> line 114, in run >> self._target(*self._args, **self._kwargs) >> File >> "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", >> line 1122, in RunLigandFit >> shutil.copyfile(mtz_in,data_local) >> File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line >> 82, in copyfile >> with open(src, 'rb') as fsrc: >> IOError: [Errno 2] No such file or directory: 'None' >> >> Evaluating LigandFit results ... >> >> Lig_seq Placed/total cc_all cc cc_adj score Code HBscore >> >> Cannot find overall_ligand_scores.log0. This could mean that none of >> that (sub)set of ligand fitted well. >> >> >> >> None of the ligand fit the difference desity well enough. Please try >> the following -- >> 1) if you input a custom library, try to use the default library (no >> extra keywords needed), or >> 2) if you used the default library already, ususlly this means that >> the density is too small (> 6 atome or more is needed.) >> Exiting ...... >> >> >> >> No good ligand found. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

8 years, 4 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Tristan Croll

To add my two cents on this: probably the second-most common question I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The honest answer to that is, "I didn't know how." Still don't, really - although the current developments are rather promising. The problem I've faced is that CCTBX was designed as its own self-contained Python (2.7, until very recently) environment, with its own interpreter and a lot of very specific environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained Python (3.7) environment. To plug one into the other in that form... well, I don't think I'm a good enough programmer to really know where to start. The move to Conda and a more modular CCTBX architecture should make a lot more possible in that direction. Pip would be even better for me personally (ChimeraX can install directly from the PyPI, but doesn't interact with Conda) - but I understand pretty well the substantial challenge that would amount to (not least being that the PyPI imposes a limit - around 100MB from memory? - on the size of an individual package). Best regards, Tristan On 2019-08-23 09:28, Luc Bourhis wrote: > Hi Graeme, > > Yes, I know. But “black" is a program doing a very particular task > (code formatting from the top of my head). Requiring to use a wrapper > for python itself is another level. But ok, I think I am mellowing to > the idea after all! Talking with people around me, and extrapolating, > I would bet that, right now, a great majority of people interested by > cctbx in pip have already used the cctbx, so they know about the > Python wrapper, and they would not be too sanguine about that. My > concern is for the future, when pip will be the first time some people > use cctbx. Big fat warning notices on PyPI page and a better error > message when cctbx fails because LIBTBX_BUILD is not set would be > needed but that could be all right. > > If we do a pip installer, we should aim at a minimal install: cctbx, > iotbx and their dependencies, and that’s it. > > Best wishes, > > Luc > > >> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk >> <Graeme.Winter(a)diamond.ac.uk> wrote: >> >> Without discussing the merits of this or whether we _choose_ to make >> the move to supporting PIP, I am certain it would be _possible_ - many >> other packages make dispatcher scripts when you pip install them e.g. >> >> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) >> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >> >> # -*- coding: utf-8 -*- >> import re >> import sys >> >> from black import main >> >> if __name__ == '__main__': >> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) >> sys.exit(main()) >> >> So we _could_ work around the absence of LIBTBX_BUILD etc. in the >> system. Whether or not we elect to do the work is a different >> question, and it seems clear that here are very mixed opinions on >> this. >> >> Best wishes Graeme >> >> >> On 23 Aug 2019, at 01:21, Luc Bourhis >> <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> Hi, >> >> Even if we managed to ship our the boost dynamic libraries with pip, >> it would still not be pip-like, as we would still need our python >> wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages >> work with the standard python exe. LD_LIBRARY_PATH, we could get >> around that by changing the way we compile, using -Wl,-R, which is the >> runtime equivalent of build time -L. That’s a significant change that >> would need to be tested. But there is no way around setting >> LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps >> there is a way to hack libtbx/env_config.py so that we can hardwire >> LIBTBX_BUILD in there when pip installs? >> >> Best wishes, >> >> Luc >> >> >> On 16 Aug 2019, at 22:47, Luc Bourhis >> <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> Hi, >> >> I did look into that many years ago, and even toyed with building a >> pip installer. What stopped me is the exact conclusion you reached >> too: the user would not have the pip experience he expects. You are >> right that it is a lot of effort but is it worth it? Considering that >> remark, I don’t think so. Now, Conda was created specifically to go >> beyond pip pure-python-only support. Since cctbx has garnered support >> for Conda, the best avenue imho is to go the extra length to have a >> package on Anaconda.org<http://anaconda.org/>, and then to advertise >> it hard to every potential user out there. >> >> Best wishes, >> >> Luc >> >> >> On 16 Aug 2019, at 21:45, Aaron Brewster >> <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >> >> Hi, to avoid clouding Dorothee's documentation email thread, which I >> think is a highly useful enterprise, here's some thoughts about >> putting cctbx into pip. Pip doesn't install non-python dependencies >> well. I don't think boost is available as a package on pip (at least >> the package version we use). wxPython4 isn't portable through pip >> (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). >> MPI libraries are system dependent. If cctbx were a pure python >> package, pip would be fine, but cctbx is not. >> >> All that said, we could build a manylinux1 version of cctbx and upload >> it to PyPi (I'm just learning about this). For a pip package to be >> portable (which is a requirement for cctbx), it needs to conform to >> PEP513, the manylinux1 standard >> (https://www.python.org/dev/peps/pep-0513/). For example, numpy is >> built according to this standard (see >> https://pypi.org/project/numpy/#files, where you'll see the manylinux1 >> wheel). Note, the manylinux1 standard is built with Centos 5.11 which >> we no longer support. >> >> There is also a manylinux2010 standard, which is based on Centos 6 >> (https://www.python.org/dev/peps/pep-0571/). This is likely a more >> attainable target (note though by default C++11 is not supported on >> Centos 6). >> >> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the >> user would need all the non-python dependencies. There's no way to >> specify these in pip. For example, cctbx requires boost 1.63 or >> better. The user will need to have it in a place their python can >> find it, or we could package it ourselves and supply it, similar to >> how the pip h5py package now comes with an hd5f library, or how the >> pip numpy package includes an openblas library. We'd have to do the >> same for any packages we depend on that aren't on pip using the >> manylinux standards, such as wxPython4. >> >> Further, we need to think about how dials and other cctbx-based >> packages interact. If pip install cctbx is set up, how does pip >> install dials work, such that any dials shared libraries can find the >> cctbx libraries? Can shared libraries from one pip package link >> against libraries in another pip package? Would each package need to >> supply its own boost? Possibly this is well understood in the pip >> field, but not by me :) >> >> Finally, there's the option of providing a source pip package. This >> would require the full compiler toolchain for any given platform >> (macOS, linux, windows). These are likely available for developers, >> but not for general users. >> >> Anyway, these are some of the obstacles. Not saying it isn't >> possible, it's just a lot of effort. >> >> Thanks, >> -Aaron >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org<mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> -- >> This e-mail and any attachments may contain confidential, copyright >> and or privileged material, and are for the use of the intended >> addressee only. If you are not the intended addressee or an authorised >> recipient of the addressee please notify us of receipt by returning >> the e-mail and do not use, copy, retain, distribute or disclose the >> information in or attached to the e-mail. >> Any opinions expressed within this e-mail are those of the individual >> and not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for >> any damage which you may sustain as a result of software viruses which >> may be transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in >> England and Wales with its registered office at Diamond House, Harwell >> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United >> Kingdom >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

6 years, 5 months

Re: [phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'

by Frank von Delft

Um, this one has been hacked to death on ccp4bb: there is in fact nothing wrong or "non-standard" with that setting. If the program won't handle it, email the authors and ask them to fix it. Reindexing is an almighty pain in the butt. That said: it sounds like you may be pointing at an out-of-date symmetry operator file; I forget which environment variable it is, check the manual, but point it to an up-to-date ccp4 installation, and I suspect it will be fine. phx On 02/02/2010 13:49, Graeme Winter wrote: > Hi Mohan, > > P22121 is not the standard setting for this spacegroup - in > International Tables the convention is to have the spacegroup's unique > axis as C, e.g. P21212 in this case. If you run this reflection file > through reindex as follows: > > reindex hklin in.mtz hklout out.mtz<< eof > reindex k,l,h > eof > > Then it should work just fine. An alternative would be to compose a > solve "symm" file and put this in the right place. This would look > something like: > > 4 Equiv positions, P22121 SG # 3018 > X,Y,Z > X,-Y,-Z > -X,1/2+Y,1/2-Z > -X,1/2-Y,1/2+Z > > (copied from spacegroup #3018 in the CCP4 symop.lib) which would need to go in > > phenix-1.6-289/solve_resolve/ext_ref_files > > On balance, reindexing is probably easiest! > > Best wishes, > > Graeme > > On 2 February 2010 13:38,<m.b.rajasekaran(a)reading.ac.uk> wrote: > >> >> Dear all, >> I have a query regarding the Autosol option in the >> PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc bound >> protein crystal with AuTOSOL. We uploaded the scaled files, sequence and all >> other details and started running AUTOSOL. But the program stopped with the >> following error message pasted below mentioning some missing of symfile. We >> were not able to locate any parameters file on the installation directory. >> It would be helpful if we get some useful suggestions on this. >> >> Thanks in advance, >> Mohan >> *********************************************************** >> >> PHENIX AutoSol Tue Feb 2 12:37:41 2010 >> >> ************************************************************ >> >> Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 >> PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : >> intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb 2 >> 12:37:41 2010 INPUT FILE LIST: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat >> >> Setting chain_type to PROTEIN Setting defaults for data_quality moderate >> Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False Setting >> max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for >> thoroughness quick Setting best_of_n_hyss_always to 1 Setting >> max_extra_unique_solutions to 0 Settin ha_iteration to No Setting >> max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to 1 >> Setting test_mask_type to No Setting n_cycle_build to 0 Setting >> thorough_loop_fit to Setting create_scoring_table to No Not truncating ha >> sites at start of resolve as this is not PHASER SAD phasing >> >> Trying to guess refinement file for later use from >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Choosing guess of refinement file for later use from all files: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_3re', >> 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)', >> 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', 'IMEAN_107_3re', >> 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', 'I_107_3re(-)', >> 'SIGI_107_3re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, >> 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_4re', >> 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)', >> 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', 'IMEAN_107_4re', >> 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', 'I_107_4re(-)', >> 'SIGI_107_4re(-)'] >> >> GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: >> (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, >> 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz >> RES: 2.5 >> >> Guess of datafile for refinement: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> >> Using >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> for refinement >> >> Specify >> input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> to change this >> >> HKLIN ENTRY: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> Inverse hand of space group: P 2 21 21 Creating sg entry from >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. >> 18) Space group name is: P 2 21 21 symbol is: p22121 >> >> **************************************** >> >> AutoSol Input failed >> >> Need a symfile for solve >> >> **************************************** >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

16 years

Re: [cctbxbb] some thoughts on cctbx and pip

by Billy Poon

Hi all, For a brief update, I have submitted a recipe for cctbxlite to conda-forge ( https://github.com/conda-forge/staged-recipes/pull/10021) and support for Python 3.7 and 3.8 is being added ( https://github.com/cctbx/cctbx_project/pull/409). With some fixes for Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. Some additional changes will be needed to get Windows to work with Python 3 and for tests to pass with Boost 1.70.0. That will enable the conda-forge recipe to build for all platforms and for all supported versions of Python. Currently, the conda-forge recipe will install into the conda python and cctbx imports can be done without sourcing the environment scripts. It looks like a lot of the environment variables being set in the dispatchers can be removed since the Python files and C++ extensions are in the right places. I'll update the libtbx_env file so that commands that load the environment can work correctly. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> wrote: > Hi Luc, > > That sounds promising. From there, I’d need to work out how to make a > fully-packaged installer (basically a modified wheel file) for the ChimeraX > ToolShed - the aim is for the end user to not have to worry about any of > this. That adds a couple of complications - e.g. $LIBTBX_BUILD would need > to be set dynamically before first import - but doesn’t seem insurmountable. > > Thanks, > > Tristan > > > > Tristan Croll > Research Fellow > Cambridge Institute for Medical Research > University of Cambridge CB2 0XY > > > > > > On 25 Aug 2019, at 18:31, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > > > > Hi Tristan, > > > > cctbx could be built to use your ChimeraX python, now that cctbx is > moving to Python 3. The option —with-python is there for that with the > bootstrap script. The specific environment setup boil down to setting two > environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, PATH > on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a framework > such as ChimeraX, that should not be difficult to ensure those two > variables are set. > > > > Best wishes, > > > > Luc > > > > > >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> wrote: > >> > >> To add my two cents on this: probably the second-most common question > I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The > honest answer to that is, "I didn't know how." > >> > >> Still don't, really - although the current developments are rather > promising. The problem I've faced is that CCTBX was designed as its own > self-contained Python (2.7, until very recently) environment, with its own > interpreter and a lot of very specific environment setup. Meanwhile I'm > developing ISOLDE in ChimeraX, which is *also* its own self-contained > Python (3.7) environment. To plug one into the other in that form... well, > I don't think I'm a good enough programmer to really know where to start. > >> > >> The move to Conda and a more modular CCTBX architecture should make a > lot more possible in that direction. Pip would be even better for me > personally (ChimeraX can install directly from the PyPI, but doesn't > interact with Conda) - but I understand pretty well the substantial > challenge that would amount to (not least being that the PyPI imposes a > limit - around 100MB from memory? - on the size of an individual package). > >> > >> Best regards, > >> > >> Tristan > >> > >>> On 2019-08-23 09:28, Luc Bourhis wrote: > >>> Hi Graeme, > >>> Yes, I know. But “black" is a program doing a very particular task > >>> (code formatting from the top of my head). Requiring to use a wrapper > >>> for python itself is another level. But ok, I think I am mellowing to > >>> the idea after all! Talking with people around me, and extrapolating, > >>> I would bet that, right now, a great majority of people interested by > >>> cctbx in pip have already used the cctbx, so they know about the > >>> Python wrapper, and they would not be too sanguine about that. My > >>> concern is for the future, when pip will be the first time some people > >>> use cctbx. Big fat warning notices on PyPI page and a better error > >>> message when cctbx fails because LIBTBX_BUILD is not set would be > >>> needed but that could be all right. > >>> If we do a pip installer, we should aim at a minimal install: cctbx, > >>> iotbx and their dependencies, and that’s it. > >>> Best wishes, > >>> Luc > >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk < > Graeme.Winter(a)diamond.ac.uk> wrote: > >>>> Without discussing the merits of this or whether we _choose_ to make > the move to supporting PIP, I am certain it would be _possible_ - many > other packages make dispatcher scripts when you pip install them e.g. > >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) > >>>> /Library/Frameworks/Python.framework/Versions/3.6/bin/black > >>>> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 > >>>> # -*- coding: utf-8 -*- > >>>> import re > >>>> import sys > >>>> from black import main > >>>> if __name__ == '__main__': > >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) > >>>> sys.exit(main()) > >>>> So we _could_ work around the absence of LIBTBX_BUILD etc. in the > system. Whether or not we elect to do the work is a different question, and > it seems clear that here are very mixed opinions on this. > >>>> Best wishes Graeme > >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto: > luc_j_bourhis(a)mac.com>> wrote: > >>>> Hi, > >>>> Even if we managed to ship our the boost dynamic libraries with pip, > it would still not be pip-like, as we would still need our python wrappers > to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages work with the > standard python exe. LD_LIBRARY_PATH, we could get around that by changing > the way we compile, using -Wl,-R, which is the runtime equivalent of build > time -L. That’s a significant change that would need to be tested. But > there is no way around setting LIBTBX_BUILD right now. Leaving that to the > user is horrible. Perhaps there is a way to hack libtbx/env_config.py so > that we can hardwire LIBTBX_BUILD in there when pip installs? > >>>> Best wishes, > >>>> Luc > >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto: > luc_j_bourhis(a)mac.com>> wrote: > >>>> Hi, > >>>> I did look into that many years ago, and even toyed with building a > pip installer. What stopped me is the exact conclusion you reached too: the > user would not have the pip experience he expects. You are right that it is > a lot of effort but is it worth it? Considering that remark, I don’t think > so. Now, Conda was created specifically to go beyond pip pure-python-only > support. Since cctbx has garnered support for Conda, the best avenue imho > is to go the extra length to have a package on Anaconda.org< > http://anaconda.org/>, and then to advertise it hard to every potential > user out there. > >>>> Best wishes, > >>>> Luc > >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto: > asbrewster(a)lbl.gov>> wrote: > >>>> Hi, to avoid clouding Dorothee's documentation email thread, which I > think is a highly useful enterprise, here's some thoughts about putting > cctbx into pip. Pip doesn't install non-python dependencies well. I don't > think boost is available as a package on pip (at least the package version > we use). wxPython4 isn't portable through pip ( > https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). > MPI libraries are system dependent. If cctbx were a pure python package, > pip would be fine, but cctbx is not. > >>>> All that said, we could build a manylinux1 version of cctbx and > upload it to PyPi (I'm just learning about this). For a pip package to be > portable (which is a requirement for cctbx), it needs to conform to PEP513, > the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For > example, numpy is built according to this standard (see > https://pypi.org/project/numpy/#files, where you'll see the manylinux1 > wheel). Note, the manylinux1 standard is built with Centos 5.11 which we > no longer support. > >>>> There is also a manylinux2010 standard, which is based on Centos 6 ( > https://www.python.org/dev/peps/pep-0571/). This is likely a more > attainable target (note though by default C++11 is not supported on Centos > 6). > >>>> If we built a manylinuxX version of cctbx and uploaded it to PyPi, > the user would need all the non-python dependencies. There's no way to > specify these in pip. For example, cctbx requires boost 1.63 or better. > The user will need to have it in a place their python can find it, or we > could package it ourselves and supply it, similar to how the pip h5py > package now comes with an hd5f library, or how the pip numpy package > includes an openblas library. We'd have to do the same for any packages we > depend on that aren't on pip using the manylinux standards, such as > wxPython4. > >>>> Further, we need to think about how dials and other cctbx-based > packages interact. If pip install cctbx is set up, how does pip install > dials work, such that any dials shared libraries can find the cctbx > libraries? Can shared libraries from one pip package link against > libraries in another pip package? Would each package need to supply its > own boost? Possibly this is well understood in the pip field, but not by > me :) > >>>> Finally, there's the option of providing a source pip package. This > would require the full compiler toolchain for any given platform (macOS, > linux, windows). These are likely available for developers, but not for > general users. > >>>> Anyway, these are some of the obstacles. Not saying it isn't > possible, it's just a lot of effort. > >>>> Thanks, > >>>> -Aaron > >>>> _______________________________________________ > >>>> cctbxbb mailing list > >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>>> _______________________________________________ > >>>> cctbxbb mailing list > >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>>> _______________________________________________ > >>>> cctbxbb mailing list > >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>>> -- > >>>> This e-mail and any attachments may contain confidential, copyright > and or privileged material, and are for the use of the intended addressee > only. If you are not the intended addressee or an authorised recipient of > the addressee please notify us of receipt by returning the e-mail and do > not use, copy, retain, distribute or disclose the information in or > attached to the e-mail. > >>>> Any opinions expressed within this e-mail are those of the individual > and not necessarily of Diamond Light Source Ltd. > >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > >>>> Diamond Light Source Limited (company no. 4375679). Registered in > England and Wales with its registered office at Diamond House, Harwell > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > >>>> _______________________________________________ > >>>> cctbxbb mailing list > >>>> cctbxbb(a)phenix-online.org > >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> _______________________________________________ > >>> cctbxbb mailing list > >>> cctbxbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/cctbxbb > >> > >> > >> _______________________________________________ > >> cctbxbb mailing list > >> cctbxbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > > _______________________________________________ > > cctbxbb mailing list > > cctbxbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

6 years, 2 months

Re: [phenixbb] phenix.refine crash -- other error

by Petrus H Zwart

Hi Ulrich, As far as I understand, you have solved the problem by sourcing the proper version of cci_apps. The files you send me look (actually glancing) fine and were not the issue. Cheers Peter ----- Original Message ----- From: Ulrich Baumann <ulrich.baumann(a)ibc.unibe.ch> Date: Monday, March 19, 2007 9:29 am Subject: Re: [phenixbb] phenix.refine crash -- other error To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Files are attached -- hope I got the right ones.... > > Quoting Petrus H Zwart <PHZwart(a)lbl.gov>: > > > This is very surprising. Not sure what happens actually. > > > > Can you please go to the directory where you have the cci_apps > sources> located, specifically, this file: > > > > /usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py > > > > and grep for > > > > select_crystal_symmetry > > > > Can you send me the build tag/version of cci_apps you installed? > That might > > make it easier for me to find out exactly what is going on ... > > > > or send me these files: > > /usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py > > /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py > > > > Sorry for this, > > > > Peter > > > > > > > > > > > > ----- Original Message ----- > > From: Ulrich Baumann <ulrich.baumann(a)ibc.unibe.ch> > > Date: Friday, March 16, 2007 4:15 am > > Subject: Re: [phenixbb] phenix.refine crash -- other error > > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > > Hi Peter, > > > > > > I hate to bother you guys with this but .... > > > > > > dcb-macbeth:[lip3] > phenix.python > > > > /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py> > data.file=lip_r3_1.8A.mtz model.file=in.pdb action=reindex > > > standard_laws=niggli#phil __OFF__ > > > ================= > > > REINDEX > > > A reindexing tool > > > ================= > > > > > > Traceback (most recent call last): > > > File > > > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",line> 468, in ? > > > reindex_utils(sys.argv[1:]) > > > File > > > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",line> 260, in reindex_utils > > > combined_xs = crystal.select_crystal_symmetry( > > > AttributeError: 'module' object has no attribute > > > 'select_crystal_symmetry' > > > > > > I seem to hae to set a spacegroup? Sorry, I could not find a > > > documentation for > > > the reindex utility. > > > > > > Many thanks, > > > > > > Ulrich > > > > > > Quoting Peter Zwart <PHZwart(a)lbl.gov>: > > > > > > > Hi Ulrich, > > > > > > > > You could try refining your structure in a primitive setting, > > > this might > > > > alleviate memory usage a bit (not sure though). > > > > > > > > try > > > > > > > > phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py > > > data.file=mydata.mtz > > > > model.file=mymodel.pdb action=reindex standard_laws=niggli > > > > > > > > You will get a new mtz file and a new pdb file. > Unfortunately, > > > the free > > > > flags are not copied over, so you would have to reindex those > > > separately > > > > using iotbx.reflection_file_converter and read that file in > > > separately > > > > in phenix.refine. > > > > > > > > This might be a bit criptic, if so, let me know and I will > post > > > more > > > > details. > > > > > > > > I am not sure this does the trick though, I hope Ralf or > Pavel > > > can give > > > > some suggestions. > > > > > > > > Cheers > > > > > > > > Peter > > > > > > > > > > > > > > > > > > > > Ulrich Baumann wrote: > > > > > Hi there, > > > > > > > > > > if you remove the ANISOU card from the input pdb file, > phenix > > > will run > > > > fine > > > > > ....sometimes not. > > > > > > > > > > phenix.refine ( Version: 2007_01_24_2154) crashed for me as > > > well: we have > > > > a > > > > > rather large unit cell and good resolution. The program > crashes> > > reproducibly > > > > > (see below) when using resolution limits better than 3 A, > although> > > sometimes > > > > > this only occurs in the 2nd macrocycle. > > > > > > > > > > Working crystal symmetry after inspecting all inputs: > > > > > Unit cell: (202.401, 202.401, 317.731, 90, 90, 120) > > > > > Space group: R 3 :H (No. 146) > > > > > > > > > > > > > > > We have 2 GB memory and could stuff in more but maybe we > can > > > limit the > > > > memeory > > > > > use in a different way? > > > > > > > > > > > > > > > Thanks a lot for your help, > > > > > > > > > > Ulrich > > > > > > > > > > > > > > > ============================= ml refinement start > > > > ============================= > > > > > > > > > > > > > > > ----------structure factors based statistics (before > > > > refinement)---------- > > > > > > > > > > Traceback (most recent call last): > > > > > File > > > > > > > > "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p>> > y", line 5, in <module> > > > > > command_line.run(command_name="phenix.refine", > > > args=sys.argv[1:])> > File > > > > > > > > "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li>> > ne.py", line 75, in run > > > > > > > > > call_back_after_monitor_collect=call_back_after_monitor_collect)> > > > > File > > > > > > > > "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py">> > , line 1108, in run > > > > > log = log) > > > > > File > > > > > > > > "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies>> > .py", line 174, in refinement_machine > > > > > abcd = abcd) > > > > > File > > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", > line> > > 185, > > > > > in __init__ > > > > > b_cart = b_cart) > > > > > File > > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", > line> > > 466, > > > > > in update_xray_structure > > > > > f_mask = > bulk_solvent_mask_obj.structure_factors(miller_set=> > > self.f_obs) > > > > > File > > > "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line > > > > 97, in > > > > > structure_factors > > > > > > > > > flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))> > > > > MemoryError > > > > > > > > > > ---------------------------------------------------------- > > > > > ------------------------------------------------------- > > > > > Quoting Pavel Afonine <pafonine(a)lbl.gov>: > > > > > > > > > >> Hi, > > > > >> > > > > >> this is known problem and it will be fixed ASAP; sorry for > this.> > > >> This presumably happens because an atom selected to > be > > > refined as > > > > >> individual anisotropic is included into a TLS group. > > > > >> I will let you know once the fixed version of CCI Apps is > > > available.> >> > > > > >> Pavel. > > > > >> > > > > >> > > > > >> > > > > >> Jianghai Zhu wrote: > > > > >>> Hi, > > > > >>> > > > > >>> I was using phenix.refine from the latest cci apps bundle > to > > > do > > > > >>> tls+individual_sites+individual_adp refinement. The > program > > > crashed > > > > >>> with the following error message. > > > > >>> > > > > >>> ----------Target weights (before refinement)- > --- > > > ------ > > > > >>> > > > > >>> > > > > >>> Traceback (most recent call last): > > > > >>> File > > > > >>> > > > > "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", > > > > >>> line 5, in <module> > > > > >>> command_line.run(command_name="phenix.refine", > > > args=sys.argv[1:])> >>> File > > > > >>> > > > > > > > > > > "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",>> >>> line 75, in run > > > > >>> > > > > call_back_after_monitor_collect=call_back_after_monitor_collect)> > > > >>> File > > > > >>> > > > > "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", > > > > >>> line 1108, in run > > > > >>> log = log) > > > > >>> File > > > > >>> > > > > "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",>> > > > > >>> line 245, in refinement_machine > > > > >>> log = log) > > > > >>> File > > > > >>> > > > > >> > > > > > > > > > > "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",>> >> > > > > >>> line 222, in __init__ > > > > >>> compute_gradients = True) > > > > >>> File > > > "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", > > > > >>> line 144, in energies_adp_aniso > > > > >>> xray_structure = xray_structure, > > > > >>> File > > > > >>> > > > > "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",>> > > > > >>> line 109, in __init__ > > > > >>> self.check_flags(fl_i) > > > > >>> File > > > > >>> > > > > "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",>> > > > > >>> line 177, in check_flags > > > > >>> assert not fl.use_u_aniso() > > > > >>> AssertionError > > > > >>> > > > > >>> Anyone has any idea what is happening? Thanks. > > > > >>> > > > > >>> Jianghai > > > > >>> > > > > >>> +++++++++++++++++++++++++++++++ > > > > >>> Jianghai Zhu, Ph.D > > > > >>> CBR Institute for Biomedical Research > > > > >>> Department of Pathology > > > > >>> Harvard Medical School > > > > >>> 200 Longwood Ave., Boston, MA 02115 > > > > >>> Ph: 617-278-3211 > > > > >>> Fx: 618-278-3232 > > > > >>> +++++++++++++++++++++++++++++++ > > > > >>> > > > > >>> > > > > >>> > > > > >>> ---------------------------------------------------------- > --- > > > ----------- > > > > >>> > > > > >>> _______________________________________________ > > > > >>> phenixbb mailing list > > > > >>> phenixbb(a)phenix-online.org > > > > >>> http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > >>> > > > > > > > > > > > > > > _______________________________________________ > > > > phenixbb mailing list > > > > phenixbb(a)phenix-online.org > > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > > > > > > -- > > > ======================================== > > > Ulrich Baumann > > > University of Berne > > > ulrich.baumann(a)ibc.unibe.ch > > > phone + 41 31 631 4320/4343 > > > fax + 41 31 631 4887 > > > > > > ------------------------------------------------------ > > > This mail was sent through IMP at http://mail.unibe.ch > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > -- > ======================================== > Ulrich Baumann > University of Berne > ulrich.baumann(a)ibc.unibe.ch > phone + 41 31 631 4320/4343 > fax + 41 31 631 4887 > > ------------------------------------------------------ > This mail was sent through IMP at http://mail.unibe.ch >

18 years, 10 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Billy Poon

Hi all, Sorry for the delayed response, I was getting the message digests to test some bulletin board settings, so I wasn't getting the individual messages for replying. For a brief update on conda, 1) External Boost libraries can now be used to build on all platforms (linux, macOS, Windows) and I'm testing updated environments with Boost 1.68 and 1.70. This is for Python 2.7, 3.6, and some initial testing on 3.7. Once 3.7 is ready, Azure Pipelines will be updated to also build 3.7. I'll do the updated dependencies as a pull request since there will be changes that stop the downloading of modules/boost. Mixing Boost versions can cause seg faults or unexpected behavior. I also did some brief testing with 1.65 since that is the minimum version that the latest versions of CUDA require. 2) The next step, like Aaron mentioned, is to get our build system to put things in more standard locations (e.g. dispatchers/binaries in $PREFIX/bin, shared libraries in $PREFIX/lib, Python source/extension modules in $PREFIX/lib/python<version>/site-packages) as a "make install" command. conda on Windows has a similar hierarchy that's specific to conda, so for Windows, this will be conda-specific. 3) Update the conda_compiler branch ( https://github.com/cctbx/cctbx_project/tree/conda_compiler). This lets the build process use the standard compilers in conda's build system. Then a CCTBX conda package can be built and added to the conda-forge channel. The conda environments for building CCTBX are already based on conda-forge dependencies. 4) With the ability to build a conda package, conda constructor ( https://github.com/conda/constructor) can be used for building our installers. This would be the more official way of packaging CCTBX with conda dependencies as a stand-alone installer. One of the roadblocks to using conda constructor was supporting noarch packages. It looks like that has been fixed ( https://www.anaconda.com/announcing-the-anaconda-2019-07-release/). So a goal for this work with conda is to make CCTBX-based programs installable as conda packages so that installing and running the software is consistent across platforms and operating system versions while also making it easier for users to add their tools to the software stack. We do have a Phenix release coming up, so I won't be able to spend much effort on this until later in September. Tristan, If ChimeraX is installable via pip, it can be installed into a conda environment. And once 2) is complete, you would be able to access CCTBX from ChimeraX. Also, this would make installing ChimeraX pretty easy for Phenix. Interestingly, the latest open source PyMOL can be built with dependencies from Schrodinger's conda channel, so it should be possible to build a conda package for PyMOL that integrates with our conda environment. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Aug 23, 2019 at 10:03 AM Tristan Croll <tic20(a)cam.ac.uk> wrote: > To add my two cents on this: probably the second-most common question > I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". > The honest answer to that is, "I didn't know how." > > Still don't, really - although the current developments are rather > promising. The problem I've faced is that CCTBX was designed as its own > self-contained Python (2.7, until very recently) environment, with its > own interpreter and a lot of very specific environment setup. Meanwhile > I'm developing ISOLDE in ChimeraX, which is *also* its own > self-contained Python (3.7) environment. To plug one into the other in > that form... well, I don't think I'm a good enough programmer to really > know where to start. > > The move to Conda and a more modular CCTBX architecture should make a > lot more possible in that direction. Pip would be even better for me > personally (ChimeraX can install directly from the PyPI, but doesn't > interact with Conda) - but I understand pretty well the substantial > challenge that would amount to (not least being that the PyPI imposes a > limit - around 100MB from memory? - on the size of an individual > package). > > Best regards, > > Tristan > > On 2019-08-23 09:28, Luc Bourhis wrote: > > Hi Graeme, > > > > Yes, I know. But “black" is a program doing a very particular task > > (code formatting from the top of my head). Requiring to use a wrapper > > for python itself is another level. But ok, I think I am mellowing to > > the idea after all! Talking with people around me, and extrapolating, > > I would bet that, right now, a great majority of people interested by > > cctbx in pip have already used the cctbx, so they know about the > > Python wrapper, and they would not be too sanguine about that. My > > concern is for the future, when pip will be the first time some people > > use cctbx. Big fat warning notices on PyPI page and a better error > > message when cctbx fails because LIBTBX_BUILD is not set would be > > needed but that could be all right. > > > > If we do a pip installer, we should aim at a minimal install: cctbx, > > iotbx and their dependencies, and that’s it. > > > > Best wishes, > > > > Luc > > > > > >> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk > >> <Graeme.Winter(a)diamond.ac.uk> wrote: > >> > >> Without discussing the merits of this or whether we _choose_ to make > >> the move to supporting PIP, I am certain it would be _possible_ - many > >> other packages make dispatcher scripts when you pip install them e.g. > >> > >> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) > >> /Library/Frameworks/Python.framework/Versions/3.6/bin/black > >> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 > >> > >> # -*- coding: utf-8 -*- > >> import re > >> import sys > >> > >> from black import main > >> > >> if __name__ == '__main__': > >> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) > >> sys.exit(main()) > >> > >> So we _could_ work around the absence of LIBTBX_BUILD etc. in the > >> system. Whether or not we elect to do the work is a different > >> question, and it seems clear that here are very mixed opinions on > >> this. > >> > >> Best wishes Graeme > >> > >> > >> On 23 Aug 2019, at 01:21, Luc Bourhis > >> <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > >> > >> Hi, > >> > >> Even if we managed to ship our the boost dynamic libraries with pip, > >> it would still not be pip-like, as we would still need our python > >> wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages > >> work with the standard python exe. LD_LIBRARY_PATH, we could get > >> around that by changing the way we compile, using -Wl,-R, which is the > >> runtime equivalent of build time -L. That’s a significant change that > >> would need to be tested. But there is no way around setting > >> LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps > >> there is a way to hack libtbx/env_config.py so that we can hardwire > >> LIBTBX_BUILD in there when pip installs? > >> > >> Best wishes, > >> > >> Luc > >> > >> > >> On 16 Aug 2019, at 22:47, Luc Bourhis > >> <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > >> > >> Hi, > >> > >> I did look into that many years ago, and even toyed with building a > >> pip installer. What stopped me is the exact conclusion you reached > >> too: the user would not have the pip experience he expects. You are > >> right that it is a lot of effort but is it worth it? Considering that > >> remark, I don’t think so. Now, Conda was created specifically to go > >> beyond pip pure-python-only support. Since cctbx has garnered support > >> for Conda, the best avenue imho is to go the extra length to have a > >> package on Anaconda.org<http://anaconda.org/>, and then to advertise > >> it hard to every potential user out there. > >> > >> Best wishes, > >> > >> Luc > >> > >> > >> On 16 Aug 2019, at 21:45, Aaron Brewster > >> <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: > >> > >> Hi, to avoid clouding Dorothee's documentation email thread, which I > >> think is a highly useful enterprise, here's some thoughts about > >> putting cctbx into pip. Pip doesn't install non-python dependencies > >> well. I don't think boost is available as a package on pip (at least > >> the package version we use). wxPython4 isn't portable through pip > >> ( > https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). > > >> MPI libraries are system dependent. If cctbx were a pure python > >> package, pip would be fine, but cctbx is not. > >> > >> All that said, we could build a manylinux1 version of cctbx and upload > >> it to PyPi (I'm just learning about this). For a pip package to be > >> portable (which is a requirement for cctbx), it needs to conform to > >> PEP513, the manylinux1 standard > >> (https://www.python.org/dev/peps/pep-0513/). For example, numpy is > >> built according to this standard (see > >> https://pypi.org/project/numpy/#files, where you'll see the manylinux1 > >> wheel). Note, the manylinux1 standard is built with Centos 5.11 which > >> we no longer support. > >> > >> There is also a manylinux2010 standard, which is based on Centos 6 > >> (https://www.python.org/dev/peps/pep-0571/). This is likely a more > >> attainable target (note though by default C++11 is not supported on > >> Centos 6). > >> > >> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the > >> user would need all the non-python dependencies. There's no way to > >> specify these in pip. For example, cctbx requires boost 1.63 or > >> better. The user will need to have it in a place their python can > >> find it, or we could package it ourselves and supply it, similar to > >> how the pip h5py package now comes with an hd5f library, or how the > >> pip numpy package includes an openblas library. We'd have to do the > >> same for any packages we depend on that aren't on pip using the > >> manylinux standards, such as wxPython4. > >> > >> Further, we need to think about how dials and other cctbx-based > >> packages interact. If pip install cctbx is set up, how does pip > >> install dials work, such that any dials shared libraries can find the > >> cctbx libraries? Can shared libraries from one pip package link > >> against libraries in another pip package? Would each package need to > >> supply its own boost? Possibly this is well understood in the pip > >> field, but not by me :) > >> > >> Finally, there's the option of providing a source pip package. This > >> would require the full compiler toolchain for any given platform > >> (macOS, linux, windows). These are likely available for developers, > >> but not for general users. > >> > >> Anyway, these are some of the obstacles. Not saying it isn't > >> possible, it's just a lot of effort. > >> > >> Thanks, > >> -Aaron > >> > >> _______________________________________________ > >> cctbxbb mailing list > >> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >> http://phenix-online.org/mailman/listinfo/cctbxbb > >> > >> _______________________________________________ > >> cctbxbb mailing list > >> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >> http://phenix-online.org/mailman/listinfo/cctbxbb > >> > >> _______________________________________________ > >> cctbxbb mailing list > >> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >> http://phenix-online.org/mailman/listinfo/cctbxbb > >> > >> > >> -- > >> This e-mail and any attachments may contain confidential, copyright > >> and or privileged material, and are for the use of the intended > >> addressee only. If you are not the intended addressee or an authorised > >> recipient of the addressee please notify us of receipt by returning > >> the e-mail and do not use, copy, retain, distribute or disclose the > >> information in or attached to the e-mail. > >> Any opinions expressed within this e-mail are those of the individual > >> and not necessarily of Diamond Light Source Ltd. > >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any > >> attachments are free from viruses and we cannot accept liability for > >> any damage which you may sustain as a result of software viruses which > >> may be transmitted in or with the message. > >> Diamond Light Source Limited (company no. 4375679). Registered in > >> England and Wales with its registered office at Diamond House, Harwell > >> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United > >> Kingdom > >> > >> _______________________________________________ > >> cctbxbb mailing list > >> cctbxbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > > _______________________________________________ > > cctbxbb mailing list > > cctbxbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

6 years, 5 months

[cctbxbb] Re: reduce2 and cell construction from python script

by Enrico Ravera

Hi all, sorry for the delay but first I had to sleep and then to teach. @Pavel, yes, the script works like a charm. @Billy, I had set the CLIBD_MON through the ccp4.setup script, but I had not finished install phenix yet. The $MMTBX_CCP4_MONOMER_LIB environmental variable has not been set by the phenix setup, but I guess this is not necessary. Many thanks again, I will hopefully come up with new questions sometimes in the future. Cheers, E. Il giorno ven 14 feb 2025 alle ore 00:01 Billy Poon <BKPoon(a)lbl.gov> ha scritto: > Hi Enrico, > > Great! Which environment variable did you set? Was it for CCP4 or for > Phenix? We should be checking some variables for restraints locations. > > And our next cctbx conda package release is at the end of this month, so > I'll add a chem_data package to the release since some tools do require > restraints. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > > On Thu, Feb 13, 2025 at 2:52 PM Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi All, >> >> I'm attaching the script the way I'd write it and that works for me. >> >> Pavel >> On 2/13/25 14:48, Enrico Ravera wrote: >> >> Hi Billy, hi all, >> I had set the environment variable for CCP4 (it is a new pc, and I did >> not have phenix installed yet), but getting chem_data solved the problem. I >> still have to figure out the next steps to saving the files, but for today >> I am happy, many thanks for your help! >> All the best, >> >> Enrico >> >> Il giorno gio 13 feb 2025 alle ore 23:40 Billy Poon <BKPoon(a)lbl.gov> ha >> scritto: >> >>> Hi Enrico, >>> >>> Do you have chem_data or access to some restraints library? It looks >>> like you are using the conda version of cctbx which does not have any >>> restraints. >>> >>> You can get a recent version of chem_data as a conda package here >>> >>> https://cci.lbl.gov/~bkpoon/chem_data-2.0rc1.5606-pyh507b02e_0.conda >>> >>> Download the file and then in your active conda environment with cctbx, >>> run >>> >>> conda install chem_data-2.0rc1.5606-pyh507b02e_0.conda >>> >>> I can confirm that with a newly created cctbx conda environment, >>> >>> mmtbx.reduce2 2gim.cif >>> >>> will fail. After installing chem_data, that command works. >>> >>> We may have to start providing the chem_data conda package on the cctbx >>> GitHub release pages. >>> >>> -- >>> Billy K. Poon >>> Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> Lawrence Berkeley National Laboratory >>> 1 Cyclotron Road, M/S 33R0345 >>> Berkeley, CA 94720 >>> Fax: (510) 486-5909 >>> Web: https://phenix-online.org >>> >>> >>> On Thu, Feb 13, 2025 at 2:14 PM Enrico Ravera <enrico.ravera(a)unifi.it> >>> wrote: >>> >>>> import sys >>>> from iotbx import pdb as pdb >>>> from mmtbx import model as mdl >>>> from mmtbx.command_line import reduce2 >>>> >>>> # Load the mmcif file >>>> model_filename = sys.argv[1] # Get the model file >>>> name from the command line >>>> protein = pdb.input(file_name=model_filename) # Load the model >>>> model = mdl.manager(model_input=protein) # Create the model manager >>>> #trim hidrogen atoms and solvent >>>> model_no_H = model.remove_hydrogens() # Remove hydrogen atoms >>>> model_no_H_no_solvent = model_no_H.remove_solvent() # Remove solvent >>>> # add hydrogens using reduce in nuclear position >>>> model_clean = reduce2(model = model_no_H_no_solvent, mode = 'nuclear') >>>> # Add hydrogens >>>> hierarchy = model_clean.get_hierarchy().expand_to_p1() # Get >>>> the hierarchy >>>> >>>> >>>> Il giorno gio 13 feb 2025 alle ore 23:08 Pavel Afonine < >>>> pafonine(a)lbl.gov> ha scritto: >>>> >>>>> Hi Enrico, >>>>> >>>>> this works for me: >>>>> >>>>> phenix.fetch_pdb 2gim >>>>> >>>>> phenix.model_statistics 2gim.cif >>>>> >>>>> mmtbx.reduce2 2gim.cif >>>>> >>>>> Something must be lost in communication. Can you provide complete set >>>>> of steps that lead to the crash? >>>>> >>>>> Pavel >>>>> On 2/13/25 13:55, Enrico Ravera wrote: >>>>> >>>>> Dear Pavel, many thanks. It ran until the reduce2 part, where it gives >>>>> the following error: >>>>> File >>>>> "/home/ravera/miniconda3/envs/cctbx/lib/python3.13/site-packages/mmtbx/monomer_library/pdb_interpretation.py", >>>>> line 1572, in resolve_unexpected >>>>> mod_mod_id = mod_dict["NH1NOTPRO"] >>>>> the file i am parsing is https://files.rcsb.org/view/2GIM.cif >>>>> >>>>> Any clues? >>>>> >>>>> Cheers, >>>>> >>>>> E. >>>>> >>>>> >>>>> Il giorno gio 13 feb 2025 alle ore 20:42 Pavel Afonine < >>>>> pafonine(a)lbl.gov> ha scritto: >>>>> >>>>>> Enrico, >>>>>> >>>>>> here are the steps (check for typos as I was typing all the below >>>>>> from >>>>>> memory): >>>>>> >>>>>> > 1) read in a mmcif file (which I think I can do following the >>>>>> tutorial); >>>>>> >>>>>> pdb_inp = iotbx.pdb.input(file_name = "4znn.pdb") # can be PDB or >>>>>> mmCIF >>>>>> model = mmtbx.model.manager(model_input = pdb_inp) >>>>>> >>>>>> > 2) trim the solvent and hydrogen atoms (probably I can do it >>>>>> following >>>>>> > the tutorial); >>>>>> >>>>>> model_no_H = model.remove_hydrogens() >>>>>> >>>>>> model_no_water = model.remove_solvent() >>>>>> >>>>>> though better: >>>>>> >>>>>> selection = model.selection("not (element H or element D or water)") >>>>>> >>>>>> model_trimmed = model.select(selection) >>>>>> >>>>>> > 3) run reduce2 to get hydrogens in the nuclear positions (no clue); >>>>>> >>>>>> Run >>>>>> mmtbx.reduce OR >>>>>> mmtbx.reduce2 OR >>>>>> mmtbx.hydrogenate >>>>>> >>>>>> to add H. I have no idea about the difference between the three >>>>>> commands >>>>>> (perhaps just the mess that someone has to finally get brave enough >>>>>> to >>>>>> clean!), but all three are supposed to add H. >>>>>> >>>>>> Also, you should be able to access the above calls programmatically, >>>>>> at >>>>>> Python script level, not running in the CL. >>>>>> >>>>>> > 4) get the full content of the unit cell (no clue). >>>>>> >>>>>> Do you mean expand to P1 (if original symmetry is not P1)? If so, then >>>>>> >>>>>> hierarchy = model.get_hierarchy().expand_to_p1() >>>>>> >>>>>> Happy to answer questions! >>>>>> Pavel >>>>>> >>>>>> _______________________________________________ >>>> cctbxbb mailing list -- cctbxbb(a)phenix-online.org >>>> To unsubscribe send an email to cctbxbb-leave(a)phenix-online.org >>>> >>> _______________________________________________ >>> cctbxbb mailing list -- cctbxbb(a)phenix-online.org >>> To unsubscribe send an email to cctbxbb-leave(a)phenix-online.org >>> >> >> _______________________________________________ >> cctbxbb mailing list -- cctbxbb(a)phenix-online.org >> To unsubscribe send an email to cctbxbb-leave(a)phenix-online.org >> >> _______________________________________________ >> cctbxbb mailing list -- cctbxbb(a)phenix-online.org >> To unsubscribe send an email to cctbxbb-leave(a)phenix-online.org >> >

11 months, 4 weeks

[phenixbb] AutoMR error

by Erik R. Kish-Trier

Hi, I am getting the following error from AutoMR, which I am fairly certain is due to the deficiencies of my machine: Python(2624) malloc: *** mmap(size=1665024000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug While using the prior release of phenix, I was able to get a similar job to complete, which makes me curious. I am running phenix 1.7-650 (GUI) on an Intel Mac with 4GB of RAM and OS 10.6.6. Any suggestions? Thanks! Erik On Feb 17, 2011, at 11:29 AM, <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> wrote: Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org<mailto:[email protected]> To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org<mailto:[email protected]> You can reach the person managing the list at phenixbb-owner(a)phenix-online.org<mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: At what percentage of saturated peaks is acceptable? (Mischa Machius) 2. Re: At what percentage of saturated peaks is acceptable? (Ed Pozharski) 3. Unrealistic number of waters found by phenix? (Ina Lindemann) 4. Re: Unrealistic number of waters found by phenix? (Folmer Fredslund) 5. Re: Unrealistic number of waters found by phenix? (Felix Frolow) 6. EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011 (Daniele de Sanctis) 7. IUCr Travel Fellowships Available (Gloria Borgstahl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 Feb 2011 20:42:55 -0500 From: "Mischa Machius" <machius(a)med.unc.edu<mailto:[email protected]>> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] At what percentage of saturated peaks is acceptable? Message-ID: <91F63968-BF15-47B4-A15E-FB73279AD18C(a)med.unc.edu<mailto:[email protected]>> Content-Type: text/plain; charset=us-ascii I would recommend taking two passes; a low-resolution pass with short exposures and a high-resolution pass with longer exposures. Then merge the two, and you've got a complete dataset. If applicable, take three or more passes. MM On Feb 16, 2011, at 8:39 PM, Jason wrote: Hi, I have a technical question that is not related to phenix, but I hope some expertise around may help me out. I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks. ====================== Jason Structural Biology Department University of Pittsburgh ====================== _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 2 Date: Wed, 16 Feb 2011 20:45:47 -0500 From: Ed Pozharski <epozh001(a)umaryland.edu<mailto:[email protected]>> To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] At what percentage of saturated peaks is acceptable? Message-ID: <1297907147.30587.17.camel@thunderclap> Content-Type: text/plain; charset="UTF-8" If you start losing completeness at low resolution, just collect a low resolution pass (i.e. exactly the same frames but with short exposures). Be mindful of radiation damage though. On Wed, 2011-02-16 at 20:39 -0500, Jason wrote: Hi, I have a technical question that is not related to phenix, but I hope some expertise around may help me out. I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks. ====================== Jason Structural Biology Department University of Pittsburgh ====================== _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 3 Date: Thu, 17 Feb 2011 08:52:26 +0100 From: Ina Lindemann <lindema2(a)staff.uni-marburg.de<mailto:[email protected]>> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Cc: heinea(a)mailer.uni-marburg.de<mailto:[email protected]> Subject: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <20110217085226.106944rzydtyujeo(a)home.staff.uni-marburg.de<mailto:[email protected]>> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 ------------------------------ Message: 4 Date: Thu, 17 Feb 2011 09:14:41 +0100 From: Folmer Fredslund <folmerf(a)gmail.com<mailto:[email protected]>> To: PHENIX user mailing list <phenixbb(a)phenix-online.org<mailto:[email protected]>> Subject: Re: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw(a)mail.gmail.com<mailto:[email protected]>> Content-Type: text/plain; charset=ISO-8859-1 Dear Ina Have a look here (from the CCP4BB) http://www.mail-archive.com/[email protected]/msg19631.html Best regards, Folmer Fredslund 2011/2/17 Ina Lindemann <lindema2(a)staff.uni-marburg.de>: Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 5 Date: Thu, 17 Feb 2011 10:23:58 +0200 From: Felix Frolow <mbfrolow(a)post.tau.ac.il> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: heinea(a)mailer.uni-marburg.de Subject: Re: [phenixbb] Unrealistic number of waters found by phenix? Message-ID: <D3ACED80-CB0C-4043-BB4A-CF8E8A936195(a)post.tau.ac.il> Content-Type: text/plain; charset=iso-8859-1 Dear Ina Lindemann These are problems of the rich people... Be happy and why not, after all your resolution is ~1.6 A I would say that you have not enough water molecules. In such resolution and such molecular size I would expect about 2 or even 3 water molecules per residue. So you are missing 198*2-334=62 water molecules. As a frequent reviewer I would not let a paper describing such structure to pass! ;-) ;-) Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Feb 17, 2011, at 09:52 , Ina Lindemann wrote: Hi, I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution. I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein. I calculated the average B of water molecules = 26.3 and protein = 12.6. Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers. With best regards, Ina Ina Lindemann Philipps-Universit?t Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------------------------------ Message: 6 Date: Thu, 17 Feb 2011 16:23:16 +0100 From: Daniele de Sanctis <de.sanctisd(a)gmail.com> To: phenixbb(a)phenix-online.org Subject: [phenixbb] EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011 Message-ID: <AANLkTikigUeBYgzF9wuJg7z5jTkZcKO0sh8j+AGUWDf6(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Deadline in 10 days!! DEADLINE TO APPLY FEBRUARY 28th COURSE ANNOUCEMENT EMBO 2011 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 6 - 10 June 2011 The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 6 to 10, June 2011. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. Confirmed invited speakers include: G. Bunkoczi, A. Cameron, D. Chirgadze, Z. Dauter, P. Evans, M. Grininger, T. Gruene, W. Kabsch, S. Panjikar, N. Pannu, A. Popov, H. Powell, L. Sazanov, G. Sheldrick, T. Terwilliger, C. Vonrhein The number of participants is limited to 20 and the deadline for application is February 28th, 2011. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://cwp.embo.org/pc11-03/ -- ????? --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869 ------------------------------ Message: 7 Date: Thu, 17 Feb 2011 10:42:00 -0600 From: Gloria Borgstahl <gborgstahl(a)gmail.com> To: phenixbb(a)phenix-online.org Subject: [phenixbb] IUCr Travel Fellowships Available Message-ID: <AANLkTik3EecaF_MB8avPPs5jZbVWjoA+s__6k067mDAD(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Please see the attachment The deadline is 15 days away. ************************************************************************ Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Professor Hobbies: ?Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, ?Crystal Perfection Interests: ?Manga, Led Zeppelin, Cold Play, piano, BRAN, RAGBRAI, golf and lately superspace groups ************************************************************************

14 years, 11 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Tristan Croll

Hi Luc, That sounds promising. From there, I’d need to work out how to make a fully-packaged installer (basically a modified wheel file) for the ChimeraX ToolShed - the aim is for the end user to not have to worry about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD would need to be set dynamically before first import - but doesn’t seem insurmountable. Thanks, Tristan Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 25 Aug 2019, at 18:31, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > > Hi Tristan, > > cctbx could be built to use your ChimeraX python, now that cctbx is moving to Python 3. The option —with-python is there for that with the bootstrap script. The specific environment setup boil down to setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a framework such as ChimeraX, that should not be difficult to ensure those two variables are set. > > Best wishes, > > Luc > > >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> wrote: >> >> To add my two cents on this: probably the second-most common question I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The honest answer to that is, "I didn't know how." >> >> Still don't, really - although the current developments are rather promising. The problem I've faced is that CCTBX was designed as its own self-contained Python (2.7, until very recently) environment, with its own interpreter and a lot of very specific environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained Python (3.7) environment. To plug one into the other in that form... well, I don't think I'm a good enough programmer to really know where to start. >> >> The move to Conda and a more modular CCTBX architecture should make a lot more possible in that direction. Pip would be even better for me personally (ChimeraX can install directly from the PyPI, but doesn't interact with Conda) - but I understand pretty well the substantial challenge that would amount to (not least being that the PyPI imposes a limit - around 100MB from memory? - on the size of an individual package). >> >> Best regards, >> >> Tristan >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: >>> Hi Graeme, >>> Yes, I know. But “black" is a program doing a very particular task >>> (code formatting from the top of my head). Requiring to use a wrapper >>> for python itself is another level. But ok, I think I am mellowing to >>> the idea after all! Talking with people around me, and extrapolating, >>> I would bet that, right now, a great majority of people interested by >>> cctbx in pip have already used the cctbx, so they know about the >>> Python wrapper, and they would not be too sanguine about that. My >>> concern is for the future, when pip will be the first time some people >>> use cctbx. Big fat warning notices on PyPI page and a better error >>> message when cctbx fails because LIBTBX_BUILD is not set would be >>> needed but that could be all right. >>> If we do a pip installer, we should aim at a minimal install: cctbx, >>> iotbx and their dependencies, and that’s it. >>> Best wishes, >>> Luc >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: >>>> Without discussing the merits of this or whether we _choose_ to make the move to supporting PIP, I am certain it would be _possible_ - many other packages make dispatcher scripts when you pip install them e.g. >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) >>>> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >>>> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >>>> # -*- coding: utf-8 -*- >>>> import re >>>> import sys >>>> from black import main >>>> if __name__ == '__main__': >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) >>>> sys.exit(main()) >>>> So we _could_ work around the absence of LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is a different question, and it seems clear that here are very mixed opinions on this. >>>> Best wishes Graeme >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >>>> Hi, >>>> Even if we managed to ship our the boost dynamic libraries with pip, it would still not be pip-like, as we would still need our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages work with the standard python exe. LD_LIBRARY_PATH, we could get around that by changing the way we compile, using -Wl,-R, which is the runtime equivalent of build time -L. That’s a significant change that would need to be tested. But there is no way around setting LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps there is a way to hack libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip installs? >>>> Best wishes, >>>> Luc >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >>>> Hi, >>>> I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. >>>> Best wishes, >>>> Luc >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >>>> Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. >>>> All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. >>>> There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). >>>> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. >>>> Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) >>>> Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. >>>> Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. >>>> Thanks, >>>> -Aaron >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> -- >>>> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. >>>> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. >>>> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> _______________________________________________ >>> cctbxbb mailing list >>> cctbxbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

6 years, 5 months

Jump to page: