- phenixbb - phenix-online.org

Re: [phenixbb] Question about Phenix refinement
by Dorothee Liebschner 12 Mar '21

12 Mar '21

Hi, This tutorial explains how to set parameters: https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s Best wishes, Dorothee On Fri, Mar 12, 2021 at 7:39 AM Zhang, Wen <wz15(a)iu.edu> wrote: > Hi, > > This is Wen from Indiana University. I have a question about the > refinement using Phenix. I got a Phenix Error, saying “Polymer crosses > special position element xxxxxxxxx. Use > allow_polymer_cross_special_position=True to keep going.” I also find this > keyword online, but am still not sure how I can change this key word. > Should I input the command somewhere? What should I do exactly? > > > > Thanks > > Wen > -- 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

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Adding hydrogens back on lipids
by Noor Agip 12 Mar '21

12 Mar '21

Hi, Is there a way to add hydrogens back on lipids using Readyset? I tried this with no success. Best wishes, Noor

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Refining ligands in a structure
by Joel Tyndall 11 Mar '21

11 Mar '21

Hi folks, It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints. Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot? I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library? phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\ Many thanks Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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Postdoctoral position in drug discovery at Vanderbilt University (Nashville, TN)
by Harp, Joel M 08 Mar '21

08 Mar '21

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein expression and purification, and all aspects of x-ray crystallography including preparation of protein-inhibitor complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experiences in molecular biology including construct design, cloning, site-directed mutagenesis, and experience with recombinant protein expression in eukaryotic cells are highly preferred. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]>

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Spatial query acceleration structure in cctbx?
by Russell M. Taylor II 08 Mar '21

08 Mar '21

As part of integrating the MolProbity tools more tightly with the CCTBX, I'm modifying the Probe code that will be shared by it and Reduce to use native CCTBX structures. One of the structures is a spatial map to accelerate the search for nearby atoms in a model. Before building my own (3D grid with near neighbors listed, ability to insert and remove atoms as they move), I wanted to check and see what was already available in the CCTBX. I looked at the page listing the CCTBX core objects and functions and did not see one, and searching for "spatial" and "accel" in the source tree did not turn up anything promising. Is there one already in there? If not, is this something that others would find to be a useful tool and, if so, where should it live? Otherwise, I'll make it part of Probe. Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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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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