Search results for "look through"

Re: [cctbxbb] bz2 support on Ubuntu

by David Waterman

Thanks, I did this, currently churning through the base build. Checking the latest Python_install_log I see hopeful-looking things like "building 'bz2' extension". I can only assume I've installed a few more packages since I did the original build. Will report back if there are any new problems, otherwise I think this might be fixed :) Cheers -- David On 8 June 2017 at 13:08, <markus.gerstel(a)diamond.ac.uk> wrote: > Hi David, > > > > You’ll have to look into the python setup.py script to figure that one out. > > https://github.com/python/cpython/blob/2.7/setup.py#L1463 > > Python expects the library to be in some fixed place, and If it’s not > there support is disabled. > > > > Regarding your rebuild question. I would keep the base_tmp directory, you > then don’t have to redownload and recompile everything. Stuff should still > recompile if anything changed, and if versions are updated etc. > > If you definitely want to recompile everything you can still save time by > running this **in the base_tmp directory**: > > find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm > –rf > > This removes all subdirectories, leaving the files intact, so you don’t > have to redownload everything. > > > > I would expect the steps *export, rm -rf base, python bootstrap.py base, > cd build, setpaths, libtbx.configure, make* to suffice. > > > > -Markus > > > > *From:* cctbxbb-bounces(a)phenix-online.org [mailto:cctbxbb-bounces@ > phenix-online.org] *On Behalf Of *David Waterman > *Sent:* 08 June 2017 12:58 > *To:* cctbx mailing list <cctbxbb(a)phenix-online.org> > *Subject:* [cctbxbb] bz2 support on Ubuntu > > > > Hi folks, > > > > My bootstrap build of cctbx/DIALS on Ubuntu 16.04.2 LTS produces a base > Python that does not have bz2 support. This is despite the fact that the > package "libbz2-dev is already the newest version (1.0.6-8)." Looking in > Python_install_log I see > > > > Python build finished, but the necessary bits to build these modules were > not found: > > _bsddb _curses _curses_panel > > _sqlite3 _tkinter bsddb185 > > bz2 dbm dl > > gdbm imageop readline > > sunaudiodev > > > > Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 > can be imported in Python? > > > > Also, what's the procedure to rebuild from base, recovering all the > currently configured modules? My guess is that something like this would do > it, but is there a better way? > > > > export MYMODULES=$(libtbx.list_modules | tr '\n' ' ') > > rm -rf base_tmp/ base/ build/ > > python bootstrap.py --builder=dials base > > python bootstrap.py --builder=dials build > > cd build > > source setpaths.sh > > libtbx.configure $MYMODULES > > make > > > > Cheers > > > -- David > > > > -- > > 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 > >

8 years, 8 months

Re: [phenixbb] red blobs (Andrea Smith)

by Pavel Afonine

Hi Andrea, here is what you can do today.. phenix.mosaic model.pdb data.mtz (yes, command line only, so far). This will take a minute or less (or more if the model is very large) and create model_mosaic.mtz file that contains the following Fourier map coefficients for mFo-DFc and 2mFo-DFc kind of maps: mFo-DFc_whole mFo-DFc_main mFo-DFc_mosaic 2mFo-DFc_whole 2mFo-DFc_main 2mFo-DFc_mosaic (you can see the MTZ file content by using this command: phenix.mtz.dump model_mosaic.mtz) The suffixes 'whole', 'main' and 'mosaic' refer to the types of masks used in calculation of each map and are explained in the paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 To reiterate: 'whole' refers to the standard default bulk-solvent mask; 'main' refers to the largest part of the standard default bulk-solvent mask (small mask droplets inside protein region are removed); 'mosaic' refers to the mosaic mask, which is essentially the 'main' mask plus only those smaller masks that contain measurable amounts of the bulk-solvent (the rest, empty ones, that are responsible for 'red blobs' are removed). Next, you load these maps and your atomic model into Coot and inspect. Artifacts such as 'red blobs' you reported earlier should be absent in 'mFo-DFc_mosaic' map. This may lead to improvement of corresponding '2mFo-DFc_mosaic' map. Now, as you can see, this is separate from refinement. Here is what you should be able to do tomorrow.. Today I will add a parameter to phenix.refine (main.mosaic=True/False), which means if you get and install tomorrow's nightly build of Phenix (dev-5285 and up) the mosaic maps, both mFo-DFc_main and 2mFo-DFc_mosaic, will be present in the MTZ file created by phenix.refine (which is available in both CL and GUI). Let me know if you have any questions! Good luck! Pavel On 3/28/24 06:24, Andrea Smith wrote: > Hi all, > > can anyone please tell me how to use the mosaic model? I went through > the phenix documentation and didn't find anything about how to use it. > > Thank you, > Andrea > > > > On Friday, March 15, 2024 22:14 CET, "Andrea Smith" > <andrea.smith(a)uochb.cas.cz> wrote: >> Hi, >> >> I went through the paper quickly during the day thinking I will have >> a thorough look at home only to realize I don't have acces to it. >> >> From the quick look it seemed that my biological background will not >> be enough to understand all of it, but I remember that it said at the >> end that the mosaic model is implemented in phenix. However, I don't >> know where. I went through the parameters in GUI and didn't find >> anything that seemed to fit the description. >> >> Could you please explain what setting I need to use in the refinement? >> >> Thank you, best, >> Andrea >> >> On Friday, March 15, 2024 16:16 CET, Pavel Afonine <pafonine(a)lbl.gov> >> wrote: >>> Hi All, >>> >>> The explanation of the reason for these blobs and the solution is both >>> detailed in depth in this paper: >>> >>> https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 >>> >>> Quick facts are: >>> >>> - These blobs are artifacts of bulk-solvent modeling. >>> - You can efficiently deal with them in Phenix. >>> - In some cases (which I witnessed myself), it is important to deal with >>> them for map improvements elsewhere (for example, in regions of >>> interest, such as ligands). >>> >>> Let me know if you have any questions! >>> >>> All the best, >>> Pavel >>> >>> >>> On 3/15/24 07:39, Mitchell D. Miller wrote: >>> > Hi Andrea, >>> > >>> > You can also put a few zero occupancy atoms in the negative >>> > density to force phenix.refine to exclude the region >>> > from the bulk solvent mask. >>> > >>> > (You may also need to set >>> > refinement.mask.ignore_zero_occupancy_atoms = False >>> > so that the zero occupancy atoms are included in the mask) >>> > >>> > Regards, >>> > Mitch >>> > >>> > >>> > >>> > Quoting Kay Diederichs <kay.diederichs(a)uni-konstanz.de>: >>> > >>> >> Hi Andrea, >>> >> >>> >> hmm, did phenix.refine actually use optimize_mask=true ? >>> >> >>> >> If you compare the logfiles of phenix.refine (for the default run >>> >> with opimize_mask=false, and the new run with optimize_mask=true) >>> >> side-by-side with xxdiff or vimdiff (yes this needs to be run from a >>> >> command-line) then there should be a difference. >>> >> >>> >> Making peace with the red blobs is somewhat unsatisfactory from a >>> >> technical viewpoint, but probably not relevant from a biological one. >>> >> >>> >> I'd guess that the authors of >>> >> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would >>> >> be interested to look at your case ... >>> >> >>> >> Best wishes, >>> >> Kay >>> >> >>> >> >>> >> Am 15.03.24 um 08:27 schrieb Andrea Smith: >>> >>> Hi Kay, >>> >>> >>> >>> I tried the mask optimization and there is no change in how the >>> >>> final map looks like. >>> >>> >>> >>> Should I just make peace with it? >>> >>> >>> >>> Best, >>> >>> Andrea >>> >>> >>> >>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs >>> >>> <kay.diederichs(a)uni-konstanz.de> wrote: >>> >>>> Hi Andrea, >>> >>>> >>> >>>> in your case, phenix.refine seems to fill bulk solvent into volumes >>> >>>> that >>> >>>> are not actually filled by solvent. >>> >>>> It might help to optimize the mask, see >>> >>>> >>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… >>> >>>> >>> >>>> "6. Mask parameters". >>> >>>> >>> >>>> Best, >>> >>>> Kay >>> >>>> -- >>> >>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >>>> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 >>> >>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >>>> >>> >>>> This e-mail is digitally signed. If your e-mail client does not >>> >>>> have the >>> >>>> necessary capabilities, just ignore the attached signature >>> >>>> "smime.p7s". >>> >>>> _______________________________________________ >>> >>>> phenixbb mailing list >>> >>>> phenixbb(a)phenix-online.org >>> >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> >> >>> >> -- >>> >> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 >>> 4049 >>> >> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >> >>> >> This e-mail is digitally signed. If your e-mail client does not >>> have the >>> >> necessary capabilities, just ignore the attached signature >>> "smime.p7s". >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 year, 10 months

Re: [phenixbb] Sharing a Phenix project via Dropbox

by Sebastiano Pasqualato

Hi Derek, I didn't have this kind of problem, and could easily install Google Drive by defining " /Google Drive " as default path. Maybe I created the directory beforehand, and then selected it while installing Google Drive, but honestly I don't remember. I think I can easily create a directory in / Best, Sebastiano > On 19/mag/2014, at 09:10, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: > > Hi Sebastian, > > Instinctively this sounded like the easiest solution of all those suggested. However when I try to do this for Dropbox through the Preferences it says "Can't create a Dropbox folder in the requested location", so it looks like it's hard-wired to use locations in my home directory. Has anyone else succeeded in moving a Dropbox folder to / ? It doesn't work for Google Drive either - it says the location is not writeable. I have administrator privileges on my Mac. Do I have to change permissions on / manually? > > Best wishes > Derek > >> On 16 May 2014, at 15:56, Sebastiano Pasqualato <sebastiano.pasqualato(a)GMAIL.COM> wrote: >> >> >> Hi Derek, >> >> the way I work with Google Drive is installing its folder (you can choose where to put it) directly into / (that is /Google Drive - unfortunately you cannot change its name and have to live with the space). >> If you and your collaborators all do that in your Macs, Phenix will find always the same path and work with no hassles. >> >> HTH, >> ciao, >> Sebastiano >> >> >>> On 16 May 2014, at 15:49, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: >>> >>> Hi Nat, >>> >>> Thanks for your reply. However could it be that it works for you because you have the same user name on each Mac, so that your home directory is always /Users/nat (or whatever)?. Thus the hard-wiring of full paths into the Phenix files would not be a problem for you? In our case there are at least 3 users with different names (in different countries!) who might want to access the same project. Otherwise I would think that Google Drive should behave just like Dropbox? >>> >>> I'm sure Jürgen's idea would work but it would be nice if possible to avoid creating a separate common user. I don't remember having done this since we had a "data processing account" on our microVAXes for integrating film data at Oxford in the early 1990s :-) Any other ideas? >>> >>> /Derek >>> >>>> On 16 May 2014, at 14:47, nathanielclar5 . <nathanielclar5(a)GMAIL.COM> wrote: >>>> >>>> Do you have the dropbox app on every computer, so that the files can be accessed through finder? I use Google Drive to sync phenix project directories between my 3 Macs, and usually it works perfectly. If I run a job on one computer, I can open a phenix gui on another, and it will show the intact job history, including jobs run on a different computer. Sometimes I get a error that 'this is not a valid phenix project directory' when I attempt to import a job folder created on a different computer. When that happens, I just make a new sub-folder within it, make that the new project folder, and move on...so maybe I'm running into the same problem as you and ignoring it. Usually it's problem free however. >>>> >>>> Nat >>>> >>>> >>>> >>>>> On Fri, May 16, 2014 at 5:03 AM, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: >>>>> Hi, >>>>> >>>>> Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! >>>>> >>>>> /Derek >>>>> >>>>> P.S. We are all using Macs. >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> web http://is.gd/IEO_XtalUnit >

11 years, 8 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Aaron Brewster

(note, power at LBL is going down now, so save more thoughts on this until Sunday afternoon, in case the messages are lost :) On Fri, Aug 16, 2019 at 4:36 PM Aaron Brewster <asbrewster(a)lbl.gov> wrote: > Hi Luc, thanks. I did recall someone working on this a while back. > > For conda, there are a couple more things to finish and then we hope to > have cctbx available through conda. > > 1) There is work being done in a branch to make cctbx use boost in > standard locations (e.g. the system boost, or a conda boost). That will > allow us to use install boost by conda and not build it ourselves. ( > https://github.com/cctbx/cctbx_project/tree/conda_boost). Also, newer > versions of boost are being tested (up through 1.70). (This will also > enable python 3.7 support.) > 2) We need to work on getting a make install step in place so that we can > build the conda package and upload it. > 3) We want to split the dependencies up by builder (cctbx, cctbx-lite, > dials, phenix, etc.) into meta packages and their associated manifests. I > can talk more about this if there is interest. > > Thanks, > -Aaron > > > > On Fri, Aug 16, 2019 at 1:48 PM Luc Bourhis <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, 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> 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 >> 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: [cctbxbb] Fwd: Re: indexing diffraction pattern

by Abbey Garant

So youre basically looking to do a search match? What inputs do you put into the software? Are these powder diffraction peaks? Laue? On Wed, Nov 14, 2018, 9:18 AM Pavel Afonine <pafonine(a)lbl.gov wrote: > Perhaps someone can reply Wen.. > > Pavel > > > -------- Forwarded Message -------- > Subject: Re: indexing diffraction pattern > Date: Sat, 10 Nov 2018 09:30:53 -0500 > From: Wen Jiang <jiang12(a)purdue.edu> <jiang12(a)purdue.edu> > To: Pavel Afonine <pafonine(a)lbl.gov> <pafonine(a)lbl.gov> > > Pavel, > Sorry for insufficient details. The scenario is that I have a numpy 2D > array of float values that represents an image of "diffraction pattern" > (generated by an image processing operation, not actual X-ray diffraction). > I need to determine the peak positions and then find a 2D lattice (two 2D > vectors) going through these peaks. I have my own simple functions that can > detect the peaks and find a 2-D lattice to cross the peaks but it often > fails when the "diffraction pattern" is not very clean. Thus, I want to > find a more robust method that works well when the peaks are relatively > weak, not very sharp, and when there are some spurious peaks off the > lattice. I think these tasks are exactly what cctbx has solved for indexing > X-ray diffraction images. > Hope that these explanations help clarify the problem. > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu > > > On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Wen, >> >> I'm not sure I fully understand your question... You say a function that >> takes a numpy array.. Array of what? >> Then, "a list of diffraction spots" -- these are measured in diffraction >> experiment. >> >> If you could provide more details as to what you are trying to do as well >> as what exactly the inputs are then I will do my best to see how to do this >> in CCTBX or forward your questions to CCTBX mailing list so that others can >> comment. >> >> All the best, >> Pavel >> >> On 11/10/18 03:56, Wen Jiang wrote: >> >> Hi Pavel, >> I am looking for a function that takes a numpy array and returns a list >> of diffraction spots and lattice vectors. I think cctbx should have such a >> function but I am not familiar with it. Can you point me in the right >> direction? >> Thanks, >> >> Wen >> >> Prof. Wen Jiang >> Department of Biological Sciences >> Department of Chemistry (Courtesy) >> Scientific Director, Purdue Cryo-EM Facility >> Purdue University >> Hockmeyer Hall of Structural Biology >> 240 S. Martin Jischke Drive >> West Lafayette, IN 47907 >> http://jiang.bio.purdue.edu >> >> >> _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

7 years, 2 months

Re: [phenixbb] Completeness issue by phenix - revisited

by Pavel Afonine

Hi Jon, please run phenix.model_vs_data mode.pdb data.mtz and that will give the the numbers for data completeness. Please send me the output of the above command if it doesn't clarify this issue. Let me know if you have any questions. Pavel. On 2/3/10 7:48 PM, Mischa Machius wrote: > Could it be that you reserved 10% of your data for Rfree and are > looking at the completeness for the work set? Do you have an > I/sigma(I) cutoff that is high? If not, it might help to post the some > of the Phenix output, e.g., the table with the completeness data along > with the resolution limits, etc. Best - MM > > On Feb 3, 2010, at 10:42 PM, J. Fleming wrote: > >> Hi, >> >> I'm having a problem using phenix.refine with my x-ray data. My >> completeness is always 89% when it should be 99%. My data was >> originally processed with CCP4i. I found an old post (see below) >> with a potential fix that doesn't work for me. I've tried changing >> the 'Anomalous flag: True' to 'Anomalous flag: False' but my >> completeness is still 89%. I've clicked through a variety of other >> setting in the GUI that I thought would help but no luck. Does anyone >> have any ideas? >> >> Thanks in advance, >> Jon >> >> >> ----- Original Message ----- >> From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> >> >> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> >> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern >> Subject: Re: [phenixbb] Completeness issue by phenix >> >> >> Hi YoungJin, >> >> I suspect phenix.refine decided your mtz file contains anomalous data >> when you actually have non-anomalous data. Could you look in the >> phenix.refine output for something like this: >> >> ================================== X-ray data ================================= >> >> >> F-obs: >> 1yjp.mtz:FOBS_X,SIGFOBS_X >> >> R-free flags: >> 1yjp.mtz:R-free-flags >> >> Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X >> Observation type: xray.amplitude >> Type of data: double, size=495 >> Type of sigmas: double, size=495 >> >> Number of Miller indices: 495 >> Anomalous flag: False >> ^^^^^ >> in particular here >> >> If you see "Anomalous flag: True" try adding this to the phenix.refine >> command line: >> >> >> xray_data.force_anomalous_flag_to_be_equal_to=False >> >> Let me know if this doesn't help. >> If it does help, I'd be interested to know how the .mtz file was >> generated. >> >> Ralf >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> 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: [phenixbb] Group ADP refinement restraints

by Pavel Afonine

Hi Taylor, you are correct, in group B factor refinement overall B factors of adjacent residues are restrained to be similar (or not too different). I will fix the documentation, thanks for pointing this out. There isn't much validation done to B factors, so dropping restraints can indeed lower R-factors but it isn't necessarily clear whether refined B factors are going to be meaningful. I guess you can try both and see what produces more meaningful B factors. Pavel On 11/25/19 16:34, Taylor Stevens wrote: > Hello, > > I am currently refining a low-ish resolution structure (through the > phenix.refine GUI) with phenix version 1.14 and had some questions > about the use of restraints in group ADP refinement. In the > phenix.refine documentation > (https://www.phenix-online.org/documentation/reference/refinement.html#refin…) > it is stated that “Group isotropic ADP or TLS refinement do not use > any restraints”, however, this does not seem to be the case. If I look > in the log file I can see the following lines of text which I believe > indicate that the restraints are being applied: > > |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = None | > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| > | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight > = 821.871| > |——————————————————————————————————————| > > If I manually set the wu parameter to 0 under “Refinement target > weights" nothing changes, however, if I navigate to "All parameters > > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” > box that is checked by default. If I uncheck this box, there are no > longer any restraints being applied according to the log file, and in > the case of the structure I am refining, there is a substantial drop > in the rfree/rwork. Is this an issue with the program or > documentation? Or am I misunderstanding how the program is supposed to > work? Is it generally a good idea to use group ADP refinement without > restraints? > > Thanks, > > Taylor > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

6 years, 2 months

Re: [cctbxbb] flex index

by Monarin Uervirojnangkoorn

Thanks!. very useful. although doesn't really work with padded array (as in the case of real_map object). but found my way round. best mona On Oct 18, 2011, at 11:17 AM, Ralf Grosse-Kunstleve wrote: > Hi Mona, > > Try this: > > from scitbx.array_family import flex > a=flex.double([1,4,5,7,5,6,6,1]) > a.set_selected(a > 5, 5) > print list(a) > > Or in smaller steps: > > bool_selection = a > 5 > assert bool_selection.size() == a.size() > print list(bool_selection) > a.set_selected(bool_selection, 5) > print list(a) > > You can also call a.set_selected(bool_selection, b) > where b is an array with as many elements as you have True in the bool_selection. > > This kind of working with selections is very typical within cctbx/phenix. > If you look through our sources you'll find a lot of examples; in passing, we have two types of selections, bool selections as above, and integer selections. The latter are useful for permutations, e.g. to sort array elements, or if you know you select only a small number of elements from a large array. Let me know if you have more questions about selections and I'll be happy to explain. (I guess one day I should write a "Working with selections" tutorial.) > > Ralf > > On Tue, Oct 18, 2011 at 2:54 AM, Monarin Uervirojnangkoorn <monarin(a)biochem.uni-luebeck.de> wrote: > Hi, > > I'm using flex and 'd like to get an access to elements fall beyond/ below certain value. eg. > a=[1,4,5,7,5,6,6,1] > anything beyond 5 should be set to 5. (in matlab then a(a>5)=5;) > if you could tell me how to do this quickly for flex, that would be great. for now i use loop and that is... pretty slow. > > many thanks. > mona > > > > ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ > Institute of Biochemistry, > Institut für Neuro- und Bioinformatik, > Graduate School for Computing in Medicine and Life Sciences > University of Lübeck, > Ratzeburger Allee 160 > Lübeck 23538 > Germany > Tel: +49451-5004072 > Fax: +49451-5004068 > > > > > > _______________________________________________ > 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 ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ Institute of Biochemistry, Institut für Neuro- und Bioinformatik, Graduate School for Computing in Medicine and Life Sciences University of Lübeck, Ratzeburger Allee 160 Lübeck 23538 Germany Tel: +49451-5004072 Fax: +49451-5004068

14 years, 3 months

Re: [cctbxbb] Module versioning (was Re: Debian Package)

by Radostan Riedel

On Sat, 01. Sep 03:33, Luc Bourhis wrote: > Now going back to patch 0007-adding-shlib-versioning, is it correct that we would just need to do: > env.Append(SHLINKFLAGS= [ "--version-info=c.r.a" ] > for the env that build a particular .so? Well, that would be for gcc and clang only of course. To be cross-platform I would suggest adding a pseudo-builder SetVersionInfo(vers) that does the right thing on Unix and nothing on Windows (for the time being, as perhaps there is a similar mechanism with msvc). That's a good idea. I'll try to rework by patch to ease everything up. > > But your well-written patch and that little sugar are the easy part as they are of the write once, reuse forever nature. We need a workflow here and the two extremes would be as follow. > > 1. Each and every cctbx developer becomes aware of so-versioning. Let's say a module is at 2.3.4, so we have > env.SetVersionInfo(vers="2.3.4") > and then a change is made to the C++ code. The developer responsible for that change should then figure out the new c.r.a and then add a comment > env.SetVersionInfo(vers="2.3.4", #next release# vers="c.r.a") > It would then be easy to automate an edit en-masse before release that would change that line and all its sisters to > env.SetVersionInfo(vers="c.r.a") > That's basically a formalised version of your proposition in your answer to Johan earlier. > > 2. Cctbx developers would not care about so-versioning and before a Debian release, the cctbx Debian maintainers would go through each call to SetVersionInfo to set the right c.r.a, based on a careful examination of the commits, complemented by asking questions to the core cctbx developers (or simply open questions on this forum). I'd of course like the first extreme better. For starters it would be great if everyone feels responsible for the "current" number. I'm not a c++ developer and I don't know if thats easy? > There are relatively very few shlibs compared to Python modules. Keeping track of the version of all of the latter by hand would be an enormous amount of work. I don't think we can get it done cheaply with some automatic keyword expansion if we want proper major.minor.patch or worse something as involved as so-versioning. Maybe it can be good to look on other projects how they are doing this. As a python developer I'm always expecting different API's when it comes to new upstream versions. I checked the policy for Debian and there seems to be nothing special in versioning extensions and modules. Maybe Justin can tell us something about Gentoo. I'd say we don't need to worry about it for now.

13 years, 5 months

[cctbxbb] Fwd: Re: indexing diffraction pattern

by Pavel Afonine

Perhaps someone can reply Wen.. Pavel -------- Forwarded Message -------- Subject: Re: indexing diffraction pattern Date: Sat, 10 Nov 2018 09:30:53 -0500 From: Wen Jiang <jiang12(a)purdue.edu> To: Pavel Afonine <pafonine(a)lbl.gov> Pavel, Sorry for insufficient details. The scenario is that I have a numpy 2D array of float values that represents an image of "diffraction pattern" (generated by an image processing operation, not actual X-ray diffraction). I need to determine the peak positions and then find a 2D lattice (two 2D vectors) going through these peaks. I have my own simple functions that can detect the peaks and find a 2-D lattice to cross the peaks but it often fails when the "diffraction pattern" is not very clean. Thus, I want to find a more robust method that works well when the peaks are relatively weak, not very sharp, and when there are some spurious peaks off the lattice. I think these tasks are exactly what cctbx has solved for indexing X-ray diffraction images. Hope that these explanations help clarify the problem. Thanks, Wen Prof. Wen Jiang Department of Biological Sciences Department of Chemistry (Courtesy) Scientific Director, Purdue Cryo-EM Facility Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 http://jiang.bio.purdue.edu On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine <pafonine(a)lbl.gov <mailto:[email protected]>> wrote: Hi Wen, I'm not sure I fully understand your question... You say a function that takes a numpy array.. Array of what? Then, "a list of diffraction spots" -- these are measured in diffraction experiment. If you could provide more details as to what you are trying to do as well as what exactly the inputs are then I will do my best to see how to do this in CCTBX or forward your questions to CCTBX mailing list so that others can comment. All the best, Pavel On 11/10/18 03:56, Wen Jiang wrote: > Hi Pavel, > I am looking for a function that takes a numpy array and returns a > list of diffraction spots and lattice vectors. I think > cctbx should have such a function but I am not familiar with it. > Can you point me in the right direction? > Thanks, > > Wen > > Prof. Wen Jiang > Department of Biological Sciences > Department of Chemistry (Courtesy) > Scientific Director, Purdue Cryo-EM Facility > Purdue University > Hockmeyer Hall of Structural Biology > 240 S. Martin Jischke Drive > West Lafayette, IN 47907 > http://jiang.bio.purdue.edu >

7 years, 2 months

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