Search results for "look through"

Re: [phenixbb] Autosol: MIRAS

by ash.k＠aol.com

Satisfactory map means: I am expecting a coiled coil or helix bundle type of assembly and I could see some densities appropriate for helices. There are proper solvent channels and continuous stretches of densities. More to add about data on this: the data is anisotropic and the longer 'c' axis and alignment of helical density along c axis support this. This also makes me think that perhaps map is sensible. Few rounds of model building, refinement and DM has been successful to assign around 10 polyala helices and their distribution looks sensible from packing point of view. Now the problem is to assign the side chain. I was hoping to make use of Se locations for this. R and Rfree are still random, in the range of 50%. I am not sure, but it could be perhaps because most of the scattering material is still unassigned. -----Original Message----- From: Francis E Reyes <Francis.Reyes(a)colorado.edu> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: phenixbb <phenixbb(a)phenix-online.org> Sent: Thu, Sep 6, 2012 8:07 am Subject: Re: [phenixbb] Autosol: MIRAS This one is solvable, but with extreme difficulty. I recently completed a structure solution with experimental phases starting at 5.0 A using phase information from multiple derivatives. How would you describe a somewhat satisfactory map? F On Sep 5, 2012, at 7:08 PM, ash.k(a)aol.com wrote: Hi Shya, I did wavelength scan, got a good signal for Se and used appropriate wavelengths for data collection and also used experimental f' and f'' values for phasing. I think the reasons SAD or MAD for SeMet data is not working are (i) low resolution: 3.7 for SeMet (Anomalous data is up to 4.8A) (ii) I should have mentioned this earlier: 3 out of 6 Se are very close to N-terminus, possible they are disordered. Unit cell is also some what big..100, 120 and 320A; F222 space group. AK -----Original Message----- From: Shya Biswas <shyabiswas(a)gmail.com> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Thu, Sep 6, 2012 7:29 am Subject: Re: [phenixbb] Autosol: MIRAS Hi AK, Did you do a wavelength scan when you collected the SE dataset you need to put the values of f' and f'' from your wavelength scan in order to locate the heavy atom sites, 6 methionine should be enough to phase your molecule. Shya On Wed, Sep 5, 2012 at 9:25 PM, <ash.k(a)aol.com> wrote: > Hi all, > > I am trying to solve a structure through experimental phasing using AUTOSOL. > I have a couple of heavy atom derivative datasets (Hg, La, Eu, Cd) and also > a SeMet data. Unfortunately all the datasets are of low resolution > (3.7-4.2A) and there are possibly 4-8 molecules in the asu. MIR, SAD and MAD > alone did not give any convincing solution. > > However, MIRAS, with a combination of few heavy atom datasets and the > anomalous data from SeMet crystals, gave a somewhat satisfactory map. But > the heavy atom site picked by AUTOSOL list only one of the heavy atoms i.e. > Lanthanum. In another set of run, the solution of which was not convincing, > the heavy atom substructure had only Hg. There are 6 Met out of 200 residues > in one molecule and mass spec results show that Se incorporation is 100%. > > Now, my doubt is that why does the heavy atom substructure contain only La > and how can I get the substructure involving Se from this solution (or the > datasets used)? Se location is going to help me a lot for finding a > starting point to assign side chains. > > Any suggestion would be greatly appreciated. > > Thanks > AK > > _______________________________________________ > 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 _______________________________________________ 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

13 years, 5 months

Re: [phenixbb] Coot mutation of Asp residue to isoAsp residue

by Zhijie Li

Hi Xiao, You need a cif file for the IAS, because IAS is not included in the standard monomer lib. Please see the attached IAS.cif I made from ASP.cif. Compared to ASP.cif, this file has the following changes: 1) compound 3-letter code to IAS, 2) compound name to 'isoASPARTIC-ACID ' 3) _chem_comp.group to L-aminoacid (so that coot won’t think it is part of a standard L-peptide and try to link next aa to the C atom. We want the CG to be linked to next N now.) The file seems to work for coot (you should be able to drag the IAS around when you have done “import CIF dictionary” with it). Hopefully it will work for refmac and phenix.refine too . Zhijie From: Xiao Lei Sent: Tuesday, August 18, 2015 1:56 PM To: Zhijie Li Cc: PHENIX user mailing list Subject: Re: [phenixbb] Coot mutation of Asp residue to isoAsp residue Hi Zhejie, For the 1AT6 structure, I downloaded its density in coot using "fetch density from EDS", but when I found the IAS at 101 position and try to do real space refine, it gives an error that "Refinement setup failure. Failed to find restraints for IAS." I do not know how to fix this but it seems to me it's caused by incomplete restraints dictionary or monomer library in ccp4? Thanks. Xiao On Tue, Aug 18, 2015 at 10:42 AM, Xiao Lei <xiaoleiusc(a)gmail.com> wrote: Hi Zhijie, Thank you very much for the information. For step 1 you mentioned, I can get monomer with L-Asp but it seems I can not drag it (or I do not know how to do) and can not delete or modify it to become isoAsp. I will try play around more though. Xiao On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li(a)utoronto.ca> wrote: Hi Xiao, IsoAsp is essentially an L-Asp linked with next aa through its side chain (beta) carboxyl. So the mutation button won’t help you. You need to build in a new L-ASP, which is treated as a covalently linked ligand (HETATM records), instead of a standard residue (ATOM records) of the protein chain. A practical method might be: 1) delete the original Asp, 2) import a free L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the density, delete one oxygen atom on the beta-carboxyl and change the residue’s numbering and chain id to fit it into the sequence, 3) edit the PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside the chain). For step 3, you may need to rename the ASP to something else (IAS was used for isoASP in older pdb, so I would go with IAS ) so that coot won’t try to make a regular peptide bond using its main chain carboxyl during real space refinement. Of course you will need to make a cif file for the “new” compound too. I guess you can make a copy of ASP.cif from the monomer library and change everything in it to IAS. I think if you have placed the IAS to the right location and its ends are in bonding distance with the neighbouring aa residues you may not need to do anything for refmac. For phenix.refine you will need to add a bond description to the .edit file for each linkage the IAS makes to the neighboring aas. You may take a look at the structure 1AT6 and its PDB file. The residue IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the chain and there are two LINK records in the header to indicate its linkage to neighbouring aas (LINK records are normally not generated or needed during refinement using refmac or phenix.refine). Zhijie From: Xiao Lei Sent: Monday, August 17, 2015 6:50 PM To: PHENIX user mailing list Subject: [phenixbb] Coot mutation of Asp residue to isoAsp residue Dear Phenixbb members, I suspect one Asp residue in my model may be an isoAsp (isomerization of Asp). I am asking if there is way to mutate Asp residue to isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in Mac OS X10.10.5)? I know there is a mutation button on coot, but the mutated aa lists are all natural amino acids. If I have to delete the Asp residue first and then build isoAsp into the density map, is there a way in coot to build an isoAsp residue in map? Thanks ahead. Xiao ---------------------------------------------------------------------------- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

10 years, 5 months

Re: [cctbxbb] bootstrap.py on windows

by richard.gildea＠diamond.ac.uk

Hallo Horst, I think this is probably a problem that the previous runs of bootstrap failed part way through building Python, and now when you're running it again it is skipping building Python because the base directory exists (and --skip-if-exists is set). However base/bin/python does not exist, so it fails. Perhaps you could try removing the base directory before re-running the script? Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Horst Puschmann [horst.puschmann(a)gmail.com] Sent: 06 April 2017 10:44 To: R. D. Oeffner Cc: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] bootstrap.py on windows Hallo Rob, Richard (Gildea) has figured this out for me -- I was using python 2.7.8 and that's the first part of the problem. I updated to 2.7.13 and the initial issues to do with ssl are solved. I am still stuck at the end: **************************************************************************** Automated CCTBX dependencies build script report problems to cctbx-dev(a)cci.lbl.gov<mailto:[email protected]> **************************************************************************** Base directory already exists and --skip-if-exists set; exiting. ===== Running in build: run configure.py Traceback (most recent call last): File "bootstrap.py", line 2113, in <module> run() File "bootstrap.py", line 2108, in run enable_shared=options.enable_shared, File "bootstrap.py", line 1036, in run i.run() File "bootstrap.py", line 189, in run raise RuntimeError("Could not run %s: File not found" % executable) RuntimeError: Could not run base\bin\python: File not found What is it looking for? Please note: this is *not* a development machine. Greetings Horst On 6 April 2017 at 10:17, R. D. Oeffner <rdo20(a)cam.ac.uk<mailto:[email protected]>> wrote: Dear Horst, I'll look into that. FYI you can also get Windows builds of CCTBX. See email below. You may have to resort using bundles from a few days ago because the two last nightly builds on windows are broken. Rob -----Original Message----- From: R. D. Oeffner Sent: Sunday, March 19, 2017 3:49 PM To: Billy Poon ; nwmoriarty(a)lbl.gov<mailto:[email protected]> Subject: Re: Windows builds for cctbx There should now be CCTBX builds for Windows in the most recent folders on http://cci.lbl.gov/cctbx_build . They are just the sources and the build directory zipped into an archive and does not include an installation program like the graphical Phenix installer for Windows. Presumably people wanting to use only CCTBX are sufficiently computer savvy to cope with this. Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html<http://www.cimr.cam.ac.uk/investigators/read/index.html> tel: +44(0)1223 763234<tel:%2B44%280%291223%20763234> mobile: +44(0)7712 887162<tel:%2B44%280%297712%20887162> -----Original Message----- From: Horst Puschmann Sent: Thursday, April 6, 2017 9:59 AM To: cctbxbb(a)phenix-online.org<mailto:[email protected]> Subject: [cctbxbb] bootstrap.py on windows Hello I am trying to install the cctbx on a Windows 7 64 bit machine using the following bootstrap.py file: https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_bu… The script will fail, unless I comment out lines 1101 and 1102: #if self.isPlatformWindows(): #tarurl, arxname, dirpath = MODULES.get_module(module)().get_tarauthenticated(auth=self.get_auth()) If it tries to execute the commented lines, the error will be "KeyError: 'cciuser' in line 590" After commenting this out, it will fail in line 271, with "AttributeError: 'module' object has no attribute '_create_unverified_context'" I can get round that with disabling line 247: if sys.platform == "win32": (i.e. change this to if sys.platform == "xxx":) After that, things start downloading. All appears well until the same thing happens again in another bootstrap.py file in \modules\cctbx_project\libtbx\auto_build\bootstrap.py If I disable *that*, it goes further but fails finally with ===== Running in build: run configure.py Traceback (most recent call last): File "bootstrap.py", line 2113, in <module> run() File "bootstrap.py", line 2108, in run enable_shared=options.enable_shared, File "bootstrap.py", line 1036, in run i.run() File "bootstrap.py", line 189, in run raise RuntimeError("Could not run %s: File not found" % executable) RuntimeError: Could not run base\bin\python: File not found I guess the automatic tests haven't picked this up, because no authentication is needed, maybe? Greetings Horst Virus-free. www.avg.com<http://www.avg.com> _______________________________________________ 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

8 years, 10 months

Re: [cctbxbb] bootstrap.py build on Ubuntu

by Billy Poon

Hi David, Sorry it look so long! Setting up all the virtual machines was a time sink and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a little tricky. It looks like Ubuntu 16.04 moved its libraries around. I used apt-get to install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1 file in /lib/x86_64-linux-gnu and in /usr/lib64. I have not gotten it to work yet, but I'm pretty sure this is the issue. I'll have to double-check 12.04 and 14.04. As for Pillow, I did test it a few months ago, but I remember there being API changes that will need to fixed. -- 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 Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman(a)gmail.com> wrote: > Hi Billy, > > I'm replying on this old thread because I have finally got round to trying > a bootstrap build for DIALS out again on Ubuntu, having waited for updates > to the dependencies and updating the OS to 16.04. > > The good news is, the build ran through fine. This is the first time I've > had a bootstrap build complete without error on Ubuntu, so thanks to you > and the others who have worked on improving the build in the last few > months! > > The bad news is I'm getting two failures in the DIALS tests: > > dials/test/command_line/tst_export_bitmaps.py > dials_regression/test.py > > Both are from PIL > > File > "/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py", > line 401, in _getencoder > raise IOError("encoder %s not available" % encoder_name) > IOError: encoder zip not available > > Indeed, from base_tmp/imaging_install_log it looks like PIL is not > configured properly > > -------------------------------------------------------------------- > PIL 1.1.7 SETUP SUMMARY > -------------------------------------------------------------------- > version 1.1.7 > platform linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32) > [GCC 5.3.1 20160413] > -------------------------------------------------------------------- > *** TKINTER support not available > *** JPEG support not available > *** ZLIB (PNG/ZIP) support not available > *** FREETYPE2 support not available > *** LITTLECMS support not available > -------------------------------------------------------------------- > > Any ideas? I have zlib headers but perhaps PIL can't find them. > > On a related note, the free version of PIL has not been updated for years. > The replacement Pillow has started to diverge. I first noticed this when > Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system python > produced failures because it no longer supports certain deprecated methods > from PIL. I worked around that in r24587, but these things are a losing > battle. Is it time to switch cctbx over to Pillow instead of PIL? > > Cheers > > -- David > > On 7 January 2016 at 18:12, Billy Poon <bkpoon(a)lbl.gov> wrote: > >> Hi all, >> >> Since wxPython was updated to 3.0.2, I have been thinking about updating >> the other GUI-related packages to more recent versions. I would probably >> update to the latest, stable version that does not involve major changes to >> the API so that backwards compatibility is preserved. Let me know if that >> would be helpful and I can prioritize the migration and testing. >> >> -- >> 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 Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter(a)lbl.gov> wrote: >> >>> David, >>> >>> I notice that the Pango version, 1.16.1, was released in 2007, so >>> perhaps it is no surprise that the latest Ubuntu does not support it. >>> Maybe this calls for stepping forward the Pango version until you find one >>> that works. I see that the latest stable release is 1.39. >>> >>> This would be valuable information for us..Billy Poon in the Phenix >>> group is supporting the Phenix GUI, so it might be advisable for him to >>> update the Pango version in the base installer. >>> >>> Nick >>> >>> Nicholas K. Sauter, Ph. D. >>> Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging >>> Division >>> Lawrence Berkeley National Laboratory >>> 1 Cyclotron Rd., Bldg. 33R0345 >>> Berkeley, CA 94720 >>> (510) 486-5713 >>> >>> On Thu, Jan 7, 2016 at 8:54 AM, David Waterman <dgwaterman(a)gmail.com> >>> wrote: >>> >>>> Hi again >>>> >>>> Another data point: I just tried this on a different Ubuntu machine, >>>> this time running 14.04. In this case pango installed just fine. In fact >>>> all other packages installed too and the machine is now compiling cctbx. >>>> >>>> I might have enough for comparison between the potentially working >>>> 14.04 and failed 15.04 builds to figure out what is wrong in the second >>>> case. >>>> >>>> Cheers >>>> >>>> -- David >>>> >>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman(a)gmail.com> >>>> wrote: >>>> >>>>> Hi folks >>>>> >>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following the >>>>> instructions here: >>>>> http://dials.github.io/documentation/installation_developer.html >>>>> >>>>> This failed during installation of pango-1.16.1. Looking >>>>> at pango_install_log, I see the command that failed was as follows: >>>>> >>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../.. >>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\" >>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\" >>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED >>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include >>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2 >>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c -fPIC >>>>> -DPIC -o .libs/fribidi.o >>>>> In file included from fribidi.h:31:0, >>>>> from fribidi.c:28: >>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or directory >>>>> >>>>> The file glib.h appears to be in base/include/glib-2.0/, however this >>>>> directory was not explicitly included in the command above, only its >>>>> parent. This suggests a configuration failure in pango to me. Taking a look >>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant >>>>> lines: >>>>> >>>>> configure:22227: checking for GLIB >>>>> configure:22235: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>> configure:22238: $? = 0 >>>>> configure:22253: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>> configure:22256: $? = 0 >>>>> configure:22304: result: yes >>>>> >>>>> but this doesn't tell me very much. Does anyone have any suggestions >>>>> as to how I might proceed? >>>>> >>>>> Many thanks >>>>> >>>>> -- David >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 > >

9 years, 7 months

Re: [phenixbb] temp files

by Billy Poon

Hi James, By default, the GUI should try to delete AutoBuild temporary files. However, if the jobs crash, the cleaning up might not take place. In that case, the deletion of temporary files can be manually run by selecting "Projects" in the menu bar, then "Clean up large files", and then selecting the project directory. -- 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 Sat, Apr 24, 2021 at 2:56 PM James Holton <jmholton(a)lbl.gov> wrote: > What if people are using the GUI ? > > On 4/24/2021 2:51 PM, Tom Terwilliger wrote: > > Hi James, > > Not the code (I hope), just any scripts that use these methods. Like this: > > mkdir /var/tmp/autosol > phenix.autosol p9.sca 2 se temp_dir=/var/tmp/autosol > > Now the temp files go in /var/tmp/autosol and the output files go in > AutoSol_run_xxx/ as usual > > All the best, > Tom > > All the best, > Tom T > > On Sat, Apr 24, 2021 at 11:59 AM James Holton <jmholton(a)lbl.gov> wrote: > >> Thank you Tom! >> >> Ok. So, in order to change the default I need to go through the code >> looking for "temp_dir" and change things? >> >> >> On 4/24/2021 10:16 AM, Tom Terwilliger wrote: >> >> Hi James, >> >> There is no overall Phenix temp directory specification, but most of the >> temp_dir usage is from autosol/autobuild/ligandfit/map_to_model. Each of >> these has the keyword "temp_dir=xxxx" which you should be >> able to set to any directory you want (and local is better as you note). >> Most programs using a temp_dir also have a keyword clean_up=True as well. >> >> All the best, >> Tom T >> >> On Sat, Apr 24, 2021 at 10:51 AM James Holton <jmholton(a)lbl.gov> wrote: >> >>> Thank you Li-Wei >>> >>> Definitely not placing blame on one program. Phenix.autobuild is another >>> big temp file producer. So is XDS. Clearly this ligand run was a case >>> of a misconfigured, runaway task that never finished. However, the files >>> lingered on disk, eating up inodes for 3 years! >>> >>> The reason I'm asking is I think there are significant performance >>> increases to be gained by using fast, local storage for scratch files. >>> This is not just in speed but storage and overall system/cluster >>> performance. Very few things are more expensive than an NFS write! >>> >>> Does anyone know how to change the default temp file location across >>> phenix ? Is this a cctbx thing? >>> >>> Thanks >>> >>> -James >>> >>> >>> On 4/23/2021 9:38 PM, Li-Wei Hung wrote: >>> > Hi James, >>> > >>> > I'll leave the global Phenix temp aspect to Billy. >>> > For ligand identification specifically, the working directory is where >>> > all the files are located. The program will purge most of the >>> > intermediate files upon completion. If the user interrupted the runs >>> > or if the program crashed at certain spots, the purge mechanism might >>> > not kick in. Even so, it'd take many runs to accumulate 20e6 (2e7?) >>> > files. In any case, you've got a point and I'll look into salvaging >>> > intermediate files of ligand identification as soon as they are not >>> > needed in the process. >>> > >>> > Thanks, >>> > >>> > Li-Wei >>> > >>> > On 4/23/2021 7:03 PM, James Holton wrote: >>> >> Hello all, >>> >> >>> >> Is there a way to configure phenix at install time (or perhaps >>> >> post-install) to put temporary files under /tmp ? I just had to >>> >> delete 20e6 temp files over NFS from a single user's phenix ligand >>> >> identification run. The delete took almost a month. >>> >> >>> >> Apologies if I am neglecting to look somewhere obvious in the >>> >> documentation, >>> >> >>> >> Happy Weekend! >>> >> >>> >> -James Holton >>> >> MAD Scientist >>> >> >>> >> _______________________________________________ >>> >> 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 >> >> >> >> -- >> Thomas C Terwilliger >> Laboratory Fellow, Los Alamos National Laboratory >> Senior Scientist, New Mexico Consortium >> 100 Entrada Dr, Los Alamos, NM 87544 >> Email: tterwilliger(a)newmexicoconsortium.org >> Tel: 505-431-0010 >> >> >> > > -- > Thomas C Terwilliger > Laboratory Fellow, Los Alamos National Laboratory > Senior Scientist, New Mexico Consortium > 100 Entrada Dr, Los Alamos, NM 87544 > Email: tterwilliger(a)newmexicoconsortium.org > Tel: 505-431-0010 > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

4 years, 9 months

Re: [phenixbb] Solving MR solution without sequence information

by Tom Peat

Hello Eric, You've had some good responses as to things to do already, but I'll throw in one 'old school' method. When I had this situation (although with somewhat higher resolution data), I went through the density with Coot and tried to put in residues where I thought I could identify them (Trp, Phe, Cys, Pro, etc). I did this iteratively (with some refinement) until I came up with a stretch of say 8-10 residues where I thought the sequence fit the density reasonably well. I then did a search for that sequence. In your case, if you obtained the protein from E. coli, then I would just search the E. coli set of proteins using something like UniProt. You obviously need to take into account that you won't be able to tell the difference between Asp/Asn and Glu/Gln, so don't look for 100% matches. This allowed me to narrow down the possible proteins to just one or two and I then had a full sequence to work with. Might be worth a shot. Best of luck, tom ________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Rosenberg, Eric (NIH/NCI) [F] <eric.rosenberg(a)nih.gov> Sent: Saturday, February 4, 2023 7:22 AM To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: [phenixbb] Solving MR solution without sequence information You don't often get email from eric.rosenberg(a)nih.gov. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi all, I’m in a bit of bind here and am seeking some advice. For context, a former graduate student in our lab set crystal trays of an MBP fusion protein, the fused part after MBP being ~400 amino acids long. This region is also predicted to be mostly unstructured, but has a C-terminal SH3 domain. Our graduate student then graduated and before throwing out some of her trays a year or two later, we found some hits of the MBP fusion protein that actually diffracted to 2.9 Angstrom. I spent some time working on it after we collected the data (June 2021), but because I didn’t know what crystallized specifically, it was impossible to phase, and replicating seemed next to impossible, too. The Matthew’s coefficient was predicting ~130 amino acids in the ASU, space group C222 or C2221. Since whatever crystallized was clearly a degradation product of the MBP fusion, I tried phasing with SH3 domains and a lot of other things to no avail. As a final last ditch effort I eventually submitted the .mtz file to SBGrid to perform a Wide Search MR job, and low and behold it actually found MR solutions that had TFZ scores ~17 in space group C2221! So here’s my current situation—I have been able to phase the data set using the MR search model, but again, I don’t know what specifically it is that I’ve crystallized. I’m currently able to get the Rfree to ~0.4, but can’t seem to improve it. I am really at a loss of what to do, since there are obvious backbone issues with the protein (as seen from iterative build composite omit maps), but every time I try to manually correct them it seems to make the Rfree worse. The MR solution does not align very well at all to the MBP fusion, only ~20 identity, and again, I don’t know to which ~130 amino acids I crystallized out of the ~400 of the MBP fusion. Is it one continuous stretch, two copies of a shorter stretch, etc.? I tried phasing with a polyalanine model of the MR search model and then tried autobuilding just a polyalanine sequence to get the backbone right, but that doesn’t seem to work. Autobuild also fails when trying to various fragments of the MBP fusion sequence. Other than opening coot and manually building the entire polypeptide chain, is there an easier method? I think that once the backbone is totally right the phases will improve so I can start putting in side chains, but I’m not sure. My latest effort is to just use Sculptor prior to Phaser in order to force the sequences to match, but again, I don’t know precisely what sequence was crystallized. I have tried both the Phenix and CCP4 software suites, for reference. Any and all help would be much appreciated (and yield an acknowledgement on a paper, if this ever works). Best, Eric Rosenberg CRTA Postdoctoral Fellow Randazzo Lab Laboratory of Cellular and Molecular Biology National Cancer Institute, US

3 years

Re: [phenixbb] alternatives to RMSD

by Morten Grøftehauge

Hi Patrick, The quick and easy way of doing this would be to use Rob Nicholls' ProSMART in CCP4. It does a local structure alignment and gives you a value for the superposition of main chain atoms. I don't know of any tool in Phenix that does this. Cheers, Morten On 8 July 2014 14:56, MARTYN SYMMONS <martainn_oshiomains(a)btinternet.com> wrote: > That's a reasonable approach and I think that it is similar to the one > used by FATCAT - which I notice is the basis for structural comparison at > the RCSB site. > Motivation and some results in the paper ( > http://www.ncbi.nlm.nih.gov/pubmed/14534198) > > It's not clear to me, though, how to fairly compare the resulting RMSD of > fragments with twists between. If I introduce an arbitrary number of > twists then I can improve the rmsd artificially. In sequence matching there > is a penalty for introducing a gap and that is scaled compared with the > amino acid substitution scoring to split the match into a 'reasonable' > number of sub-alignments. Obviously in 3D case there should also be a > penalty for introducing a split in the structure to do a twist > re-orientation - but how to quantify it compared with RMSD and get a global > score? > > Seems to me better would be to express the whole problem in torsional > space - so the twists would be large displacements while the matched > sections should have close fit in torsional angles. And a global score > could be calculated. Someone must have tried this? > > All the best > Martyn > Cambridge > ----Original message---- > From : tg(a)shelx.uni-ac.gwdg.de > Date : 07/07/2014 - 11:47 (GMTDT) > To : phenixbb(a)phenix-online.org > Subject : Re: [phenixbb] alternatives to RMSD > > Hi Patrick, > > why don't you superimpose only the matching segments and report their > RMSD? It is the common procedure for RMSD's from superpositions to > report the aligned residues together with the RMSD. > > The advantage compared to a map CC is similar to that of R_sym over > R_meas: readers have a better concept (from experience) of what the > numbers mean. > > Best, > Tim > > On 07/02/2014 05:15 PM, Patrick. C wrote: > > Hi Phenix users, > > > > I am not a crystallographer but I though you guys might be a good place > to ask > > this question. > > > > I have 2 super secondary structures, A and B and they consist of > Helix-turn-Strand > > > > Due to the turn the two structures have a poor RMSD because the two > flanking > > fragments of Helix and Strand are far from each other but when I > superimpose the > > two fragments individually(helixA with helix B and standA with strandB > in Pymol > > they align very well). > > > > Now, is there a way to express this instead of using the RMSD? > > When the two structures align well the RMSD is very good but a slight > movement > > and the RMSD is awful. > > But looking at the two structures I can see they follow the same path > through space. > > > > Thank you, > > Patrick > > > > > > > -------------------------------------------------------------------------------- > > 3D Earth Screensaver Preview <http://www.inbox.com/earth> > > *Free 3D Earth Screensaver* > > Watch the Earth right on your desktop! Check it out at > www.inbox.com/earth > > <http://www.inbox.com/earth> > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > _______________________________________________ > 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 > -- Morten K Grøftehauge, PhD Pohl Group Durham University

11 years, 6 months

Re: [phenixbb] helix/sheet outliers

by Oleg Sobolev

Hi Casper, > I am doing real space refinement on a protein model build from a cryo-em > map. I run the refinement with Amber gradients turned on and with secondary > structure restraints (otherwise, more or less default settings). > Amber gradients should not be relevant to the issue. SS filtration is based on input model geometry before any coordinate refinement was done. > I have some issues with helix and sheet outliers. > > Every time I run the refinement (after making sure that the bond distance > in the helices are within the 3.5 Å) > I get a lot of bad annotation remarks, but with outliers just above 3.5 Å > (see .log below): > > > > … > > removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " > (cutoff:3.500A) > > Proline residue: A 180 - end of helix > > removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A > 184 " (cutoff:3.500A) > > removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A > 185 " (cutoff:3.500A) > > removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A > 186 " (cutoff:3.500A) > > Processing helix chain 'A' and resid 219 through 228 > > removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A > 223 " (cutoff:3.500A) > > … > > > > Is this something that I just need to fix in several rounds of refinement > or is there an explanation? > If you believe the distances you see in the log are wrong, I'm happy to investigate. Please send me the model file (off-list) with an explanation why do you think so. The distances (even 3.5) suggest a rather poor helix geometry since the target distance is 2.9A. If you are sure your annotations are correct, you may try to relax the threshold by setting parameter "distance_cut_n_o" to some larger value than default 3.5. Then the restraints will be imposed and hopefully the geometry of the helix will become good during refinement. > In addition, I have some bad sheet annotations such as: > > > > … > > removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " > (cutoff:3.500A) > > removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B > 431 " (cutoff:3.500A) > > removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B > 442 " (cutoff:3.500A) > > removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B > 429 " (cutoff:3.500A) > > removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B > 444 " (cutoff:3.500A) > > … > > > > When I look at the model, the residues are definitely a part of the sheet > – the long distance between the N-O atoms is due to the O being “flipped” > (hope it makes sense). > > Is this because of wrong annotation? > If you believe the residues are part of the sheet - then the annotation is correct, the model is wrong. If you believe the O needs to be "flipped" - go ahead and flip it. Do any other adjustments you deem necessary to improve the model and hydrogen-bonding pattern. This may result in proper distance between N and O and established restraint. Such big model changes are better done manually rather than during refinement with restraints. Some relevant tutorials are: https://www.youtube.com/watch?v=9dCkAdR1RDk&feature=youtu.be https://www.youtube.com/watch?v=qB8W_6yuw5k&feature=youtu.be Relevant documentation and links in it: https://www.phenix-online.org/documentation/reference/secondary_structure.h… Please let us know if you have more questions. Best regards, Oleg Sobolev. > > > > > Best > > Casper > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

5 years, 9 months

Re: [cctbxbb] Making branches by accident

by Nigel Moriarty

Markus I was a non-rebaser but I have set it to true on my second machine. So my question is regardind branches. I have made a branch, made some changes and merged the master into the branch. I will make some more changes during testing. I assume that I merge into the master at some point. Will the commits appear in the log based on the time of the merge or the time I committed in the branch? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Dec 8, 2016 at 12:14 AM, <markus.gerstel(a)diamond.ac.uk> wrote: > I use a custom prompt so I can see what is going on when I am in a git > repository folder. > > This is the code one could add to their ~/.bashrc: > https://gist.github.com/Anthchirp/dfc9a4382f8dfc9a97fe1039c9e6789a > > This is what it looks like: > https://postimg.org/image/8c9h72qwd/ > > This is what happens in the image: > * yellow brackets indicate you are in git territory, and contain the > current branch name > * red branch name = uncommitted changes in repository > * positive number: number of commits the local repository is ahead of the > remote repository > * the 'git pull' command causes an implicit merge commit, which I undo > with the next command > * negative number: number of commits the local repository is behind the > remote repository > * both negative and positive number: branches have diverged > > Maybe someone finds it useful. > > -Markus > > > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] > on behalf of Pavel Afonine [pafonine(a)lbl.gov] > Sent: Wednesday, December 07, 2016 18:24 > To: cctbxbb(a)phenix-online.org > Subject: Re: [cctbxbb] Making branches by accident > > This happened to me a few times now, and just double-checked that my > .gitconfig contains "rebase = true". Let's see if it happens again.. > Pavel > > On 12/7/16 00:02, Graeme.Winter(a)diamond.ac.uk<mailto: > Graeme.Winter(a)diamond.ac.uk> wrote: > Morning all > > I am seeing a certain amount of “Merge branch 'master' of github.com: > cctbx/cctbx_project” coming through on the commits – this usually means > you did not do a git pull –rebase before the git push. This can be set to > the default by using the spell Markus sent out > > git config --global pull.rebase true > > This will need to be done on each machine you push from, else getting the > habit of doing a git pull –rebase before push is a good one. > > We have had this on and off with DIALS but it tends to pass easily enough. > > What bad happens? Nothing really but the history becomes confusing… > > So: may be worth checking that you have the pull.rebase thing set? > > Cheerio Graeme > > > > -- > > 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<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

9 years, 2 months

Re: [phenixbb] reflection file utility and use of modified phases in refinement

by Engin Ozkan

Hi Tom, My second question was about autobuild recommending modified phases to be used in further refinement. This is the end of the log file printed by autobuild. See the line for "Data for refinement": Summary of output files for Solution 3 from rebuild cycle 4 --- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_4.pdb --- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_4.log_refine --- Model-building log file --- log: AutoBuild_run_1_/cycle_best_4.log --- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_4.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PH FOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_4.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz --- Density-modification log file --- log_denmod: AutoBuild_run_1_/cycle_best_4.log_denmod --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_4.mtz If HLAM, HLBM, HLCM and HLDM are density-modified phases, it looks like that's what autobuild suggests. Thanks again, Engin On 8/28/09 7:07 AM, Thomas C. Terwilliger wrote: > Hi Engin, > > I'm not sure about your main question...I hope that Nat or Pavel will > answer you on that. > > On the use of density-modified phases in refinement: AutoBuild expects > experimental phases in the data file, with experimental HL coefficients, > and it by default it will use those HL coefficients in refinement with an > MLHL target. > > The phase probabilities from resolve statistical density modification are > pretty accurate, and not inflated, so you could use them in refinement if > you wanted to. I don't suggest it, however, because the > density-modification phase information is not fully independent of the > other information used in refinement (e.g., a flat solvent is implicit in > your refinement already, so including that through density modification is > partially redundant). > > ps: I hope AutoBuild doesn't recommend using density-modified phases in > refinement, so if you could send me the text where it says that, I will > check that out! > > All the best, > Tom T > > >>> Hi everybody, >>> >>> I had some trouble with the reflection file utility today. I've been >>> trying to import Rfree-flag column from one of the mtz's to my combined >>> mtz, and it never does. The R-free flag is always left out of the output >>> even when I have it selected. Have you guys seen this (I'm using 147)? >>> >>> Another question I have is about the output of phenix.autobuild. >>> Phenix.autobuild tells me to use modified phase probabilities (HLAM, >>> etc.) in refinement. I am assuming this is density-modified phases. But >>> I've always thought that this would be bad practice (possibly because of >>> unrealistically high FOMs and possible flattening of loops, etc, but >>> maybe resolve does a better job than, say DM). Any ideas on that one? >>> >>> Thanks, >>> >>> Engin >>> >>> -- >>> Engin Özkan >>> Post-doctoral Scholar >>> Dept of Molecular and Cellular Physiology >>> Howard Hughes Medical Institute >>> Stanford University School of Medicine >>> ph: (650)-498-7111 >>> >>> _______________________________________________ >>> 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 > -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

16 years, 5 months

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