- phenixbb - phenix-online.org

PAIREF Webinar (23rd March 2021, 15:00 CET)
by Petr Kolenko 08 Mar '21

08 Mar '21

Dear colleagues, We are pleased to announce the webinar on paired refinement to be held on March 23, 2021, from 3 PM (CET) to 4 PM (CET). This protocol provides an accurate estimation of the high-resolution cutoff (https://journals.iucr.org/m/issues/2020/04/00/mf5044/). The "PAIREF webinar" will be a free virtual event for up to 300 participants. The meeting will be recorded. Please register and receive your Zoom link here: https://kipl-indico.fjfi.cvut.cz/e/pairef We will cover: 1. Introduction to paired refinement. 2. Installation of PAIREF for CCP4 and/or PHENIX users. 3. Short tutorial (files will be provided). 4. Discussion. Feel free to contact us with your data. Best regards, Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek

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error for "rosetta.run_tests"
by Smith Lee 06 Mar '21

06 Mar '21

Dear All, For rosetta installation for use in phenix, in the .bashrc I have: export PATH="/home/usrname/rosetta_src_2020.08.61146_bundle":$PATHexport PATH="/home/username/phenix11914122installdir/phenix-1.19.1-4122/build/bin":$PATH and I have the .bashrc file sourced. However when I run "rosetta.run_tests", I got the following error: --...... End of input processing Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. ---- I am looking forward to getting your advice on how to solve the error issue. Smith

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phenix.molprobity geo
by Paul Emsley 04 Mar '21

04 Mar '21

Hello, I'd like to compare the restraints generated by Coot to the validation provided by molprobity. When I run phenix.molprobity on my model, it gives me (amongst other things) this: ----------------------- Histogram of nonbonded interaction distances: 1.87 - 2.42: 526 2.42 - 2.96: 3217 2.96 - 3.51: 3639 3.51 - 4.05: 5026 4.05 - 4.60: 6847 Nonbonded interactions: 19255 Sorted by model distance: nonbonded pdb=" O LEU A 21 " pdb=" H GLY A 26 " model vdw 1.874 1.850 nonbonded pdb=" H ILE A 71 " pdb=" O TYR A 80 " model vdw 1.920 1.850 nonbonded pdb=" H GLY A 34 " pdb=" O GLU A 54 " model vdw 1.925 1.850 nonbonded pdb=" O ILE A 71 " pdb=" H TYR A 80 " model vdw 1.937 1.850 nonbonded pdb=" HE ARG A 40 " pdb=" HG1 THR A 76 " model vdw sym.op. 1.955 2.100 -x+3/2,-y,z+1/2 ... (remaining 19250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. -------------------------- I don't understand this lilst. Should I be concerned by those interactions? Which of these atom pairs are contributing to the clashscore? Perhaps the details are in the .geo file? How do I get a .geo file? I googled, I didn't find the answer. How could I have found the answer without asking here? Thanks, Paul.

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Re: [phenixbb] executing Phenix in a python script on a Windows OS
by Muriel Gelin 02 Mar '21

02 Mar '21

Here is what I have: In a prompt: C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat C:\Users\MG>phenix.refine Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file] -------------------------------------------------------------------------------- In python: source = subprocess.Popen(str(r"C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat"), stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) >>> phenix.refine Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'phenix' is not defined >>> py phenix.refine File "<stdin>", line 1 py phenix.refine ^ -------------------------------------------------------------------------------- If somebody see what is the problem. I'm afraid I am stuck ... Thank you all. Muriel Le 02/03/2021 à 11:03, gelin a écrit : > Dear Bernhard, > > Thank you for your answer. > > Executing phenix_env.bat in Windows command prompt works well, since I > can then execute phenix.refine in the prompt. > > So I tried to add in my python script something like that: > source = subprocess.Popen(my_path\phenix_env.bat, > stdin=subprocess.PIPE, stdout=subprocess.PIPE, > stderr=subprocess.PIPE) > Unfortunately, it doesn't work. I suppose the prompt environment is > not modified. > > Do you know how to do that in my python script so that I can then > execute something like: > xtriage = subprocess.Popen(["phenix.xtriage", my_mtz, > "parameters.reporting.log=" + "xtriage.log")], > stdin=subprocess.PIPE, > stdout=subprocess.PIPE, stderr=subprocess.PIPE) > > Thank you for you help. > > Muriel > > Le 2021-03-01 18:36, Bernhard Rupp a écrit : >> Here is what I did: >> >> Install phenix >> >> make a batch command in your path (eg phx.bat) that executes the >> environment setup, eg. >> C:\Phenix\phenix-installer-1.19-4092-intel-windows-x86_64\phenix_env.bat >> >> Open terminal, execute that batch (modify as you like), and there you go >> >> c:\data\Dropbox\Refinements\5okl>phenix.refine >> Usage: phenix.refine [options] [reflection_file] [pdb_file] >> [parameter_file] >> .... >> >> Best, BR >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org >> <phenixbb-bounces(a)phenix-online.org> On Behalf Of Muriel Gelin >> Sent: Monday, March 1, 2021 09:08 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] executing Phenix in a python script on a Windows OS >> >> Dear Phenix community, >> >> I wrote a python script to automate the processing of our data with >> Phenix. I'm not a developer by profession, but a crystallographer, and >> write scripts usually under Linux. My colleagues working under Windows >> asked me to share my script. >> >> I managed to run a simple python script under windows, no problem. But >> for a script that executes Phenix, it's not so easy (for me). >> >> Under Linux, I manage to source phenix_env.csh, but under Windows what >> is the command to setup Phenix in order to simply use phenix.refine >> or phenix.xtriage in my script? >> >> All I can find is this page >> https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html >> >> >> but I don't think it answers my question. >> >> Thank you in advance for your help! >> >> Muriel >> >> -- >> Dr Muriel Gelin >> >> Research Engineer >> Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced >> Biology, Chemistry, Informatics Studio" >> >> CNRS UMR 5048 - UM - INSERM U 1054 >> 29 rue de Navacelles >> 34090 MONTPELLIER Cedex - FRANCE >> http://www.cbs.cnrs.fr >> >> Tel: (33) 04 67 41 77 12 >> >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix
by Smith Lee 02 Mar '21

02 Mar '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Computational Crystallography Newsletter – Jan. 2021
by Nigel Moriarty 01 Mar '21

01 Mar '21

Folks The latest issue of the CCN is available on the website. Please consider contributing to future issues. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. January 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf> Articles - HKLviewer, a new 3D reflection data viewer for CCTBX <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=15> - Running CCTBX and PyMOL in the same Jupyter Notebook <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=26> Short Communications - PDB50: Celebrating 50 Years of the Protein Data Bank in 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=5> - Lessons from using the Cambridge Structure Database: II – Element specification X/Z <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=6> - The Importance of Being Positive: Charged ligands that bind nucleic acids <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=9> Fitting tips #20 - In-plane or out-of-plane H atom placement on the edges of aromatic rings <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=2> 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 ORCID : orcid.org/0000-0001-8857-9464

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executing Phenix in a python script on a Windows OS
by Muriel Gelin 01 Mar '21

01 Mar '21

Dear Phenix community, I wrote a python script to automate the processing of our data with Phenix. I'm not a developer by profession, but a crystallographer, and write scripts usually under Linux. My colleagues working under Windows asked me to share my script. I managed to run a simple python script under windows, no problem. But for a script that executes Phenix, it's not so easy (for me). Under Linux, I manage to source phenix_env.csh, but under Windows what is the command to setup Phenix in order to simply use phenix.refine or phenix.xtriage in my script? All I can find is this page https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html but I don't think it answers my question. Thank you in advance for your help! Muriel -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix use
by Smith Lee 28 Feb '21

28 Feb '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Collection of articles from ISDSB2019 now published in IUCr Journals
by John R Helliwell 26 Feb '21

26 Feb '21

Dear Colleagues, A collection of articles from the International Symposium on Diffraction Structural Biology 2019 held in Osaka is now online in IUCr Journals at https://journals.iucr.org/special_issues/2021/ISDSB2019 Several of these articles are open access. Best wishes, Atsushi Nakagawa, John Helliwell and Yuriko Yamagata

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NCS/pseudo-symmetry
by Muhammad Bashir Khan 25 Feb '21

25 Feb '21

Dear All; *I collected data set which can be easily processed in a space grouop P21 (P1211)* *at approx 3.7A. I procedeed with MR using phaser in phenix which give a solution with two copies. * ** There were 8 solutions ** Pdb and/or Mtz files have been written with results for 1 of these solutions ** Solution #1 written to PDB file: Khan_phaser.1.pdb ** Solution #1 written to MTZ file: Khan_phaser.1.mtz Solution #1 annotation (history): SOLU SET RFZ=3.4 TFZ=4.2 PAK=0 LLG=15 TFZ==5.5 RFZ=2.8 TFZ=27.6 PAK=5 LLG=1173 TFZ==36.5 LLG=1210 TFZ==36.8 PAK=6 LLG=1210 TFZ==36.8 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.3 FRAC 0.20 0.00 0.18 BFAC -1.90 #TFZ==5.5 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.2 FRAC 0.05 0.00 0.51 BFAC 1.60 #TFZ==36.8 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64 Solution #2 annotation (history): SOLU SET RFZ=3.0 TFZ=5.5 PAK=0 LLG=10 RFZ=2.7 TFZ=25.6 PAK=0 LLG=1165 TFZ==34.8 LLG=1198 TFZ==34.0 PAK=4 LLG=1198 TFZ==34.0 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00 0.14 BFAC -3.15 SOLU 6DIM ENSE ense_1 EULER 169.3 96.4 357.9 FRAC 0.91 -0.00 0.52 BFAC 1.82 #TFZ==34.0 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65 Solution #3 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=34.6 PAK=1 LLG=1146 TFZ==39.7 LLG=1185 TFZ==39.2 PAK=3 LLG=1186 TFZ==39.2 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00 0.01 BFAC -1.69 SOLU 6DIM ENSE ense_1 EULER 8.3 86.4 2.0 FRAC -0.14 -0.00 0.34 BFAC 1.72 #TFZ==39.2 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64 Solution #4 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=2.9 TFZ=30.5 PAK=6 LLG=1156 TFZ==34.4 LLG=1183 TFZ==33.6 PAK=7 LLG=1183 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00 0.47 BFAC -2.89 SOLU 6DIM ENSE ense_1 EULER 359.5 82.1 2.8 FRAC -0.02 -0.00 0.14 BFAC 2.57 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64 Solution #5 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=3.0 TFZ=29.0 PAK=6 LLG=1115 TFZ==34.1 LLG=1178 TFZ==33.6 PAK=7 LLG=1178 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00 0.47 BFAC -1.57 SOLU 6DIM ENSE ense_1 EULER 180.1 99.2 180.7 FRAC 0.34 0.50 0.20 BFAC 2.47 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64 Solution #6 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=36.2 PAK=1 LLG=1136 TFZ==35.0 LLG=1169 TFZ==34.6 PAK=1 LLG=1169 TFZ==34.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01 0.03 BFAC -2.58 SOLU 6DIM ENSE ense_1 EULER 359.2 82.9 1.4 FRAC -0.09 0.01 0.36 BFAC 2.08 #TFZ==34.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66 Solution #7 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=35.3 PAK=1 LLG=1122 TFZ==35.4 LLG=1149 TFZ==34.5 PAK=1 LLG=1148 TFZ==34.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01 0.03 BFAC -1.93 SOLU 6DIM ENSE ense_1 EULER 180.8 97.5 182.4 FRAC 0.78 -0.49 0.31 BFAC 2.44 #TFZ==34.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65 Solution #8 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=33.9 PAK=1 LLG=1083 TFZ==38.5 LLG=1146 TFZ==38.5 PAK=4 LLG=1146 TFZ==38.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00 0.00 BFAC -1.77 SOLU 6DIM ENSE ense_1 EULER 8.1 86.2 2.6 FRAC 0.17 -0.00 -0.33 BFAC 1.66 #TFZ==38.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65 CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs) Finished: Tue Feb 16 23:27:36 2021 *Got the following warnings:* WARNINGS -------- ------------------------------------------------------------------------------------------ Warning: Intensity moments suggest possibility of twinning. Tests based on possible twin laws will be more definitive. ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------ Warning: The composition you have entered gives a solvent content of 87%, which is extremely unlikely. You should increase the composition. After running xtraige for the .mtz, I get this warning about NCS Frac. coord. : 0.157 -0.000 -0.333 Distance to origin : 119.294 Height relative to origin : 33.056 % p_value(height) : 8.504e-04. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Upon an attempt at initial refinement with different stratageis, the R-fators are stuck at Start R-work = 0.5066, R-free = 0.5233 Final R-work = 0.4831, R-free = 0.4965 The question is that there is something that is not being recognized for example merohedral twinning or that the NCS/pseudosymmetry is not being addressed correctly. Any suggestions would be highly appreciated. Regards; Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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