- phenixbb - phenix-online.org

wwPDB ligand validation updates
by John Berrisford 12 Jun '19

12 Jun '19

Hi Our recent update to the wwPDB validation reports provides much clearer validation information for ligands. We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by X-ray crystallography, 3-dimensional views of electron density. We also provide calculated electron density map coefficients which were used to generate the analysis in the validation reports. Initially, the updated-style reports will be available to in deposition, and publicly for newly released or updated PDB entries. The new features will be available for the whole archive following the next archive-wide recalculation validation reports. For more information, please visit https://www.wwpdb.org/news/news?year=2019#5cfa7992ea7d0653b99c87d0 Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

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Phenix cryo-em tools workshop
by Ahmad Khalifa 07 Jun '19

07 Jun '19

Someone posted about a one day workshop for the cryo-em tools in Phenix. I can't seem to find this email, can someone please pass me a link to the workshop? Regards.

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Postdoc Opening - Multi-Dataset Crystallography and Allostery - Keedy Lab, New York City
by Daniel Keedy 03 Jun '19

03 Jun '19

The Daniel Keedy Lab at the CUNY Advanced Science Research Center in New York City has an available position for a Postdoctoral Researcher starting immediately. The Keedy Lab aims to elucidate the conformational ensembles of proteins and to understand how they are shifted by perturbations, including mutations, protein:protein interactions, and ligands, to control function. We are especially interested in how “hidden” conformational ensembles drive differences in allosteric regulatory mechanisms for protein tyrosine phosphatases (PTPs), which are under-studied but biologically critical. To explore these questions, we are developing new multi-dataset approaches in X-ray crystallography that couple advances in automated data collection and multi-state modeling algorithms. For more information, visit our newly designed lab website: www.keedylab.org<http://www.keedylab.org> The ideal applicant should have a strong background in macromolecular X-ray crystallography, whether experimental, computational, or both. Experience writing or contributing to scientific software is also preferred. Candidates with other expertise in biophysics, computational biology, or related areas are also welcome to apply. The CUNY Advanced Science Research Center is a new cutting-edge research institution located in upper Manhattan in New York City -- the "greatest city in the world". The Structural Biology Initiative of the ASRC features seven tenure-track and research-track faculty members, pursuing diverse research problems using X-ray diffraction, cryo-EM, NMR, mass spectrometry, solution biophysics, and advanced microscopy. The ASRC is immediately adjacent to the New York Structural Biology Center, a consortium of CUNY and eight other New York academic institutions with world-class facilities, and 70 miles from Brookhaven National Laboratory, featuring the newly constructed National Synchrotron Light Source II, now the brightest synchrotron light source in the United States. The ASRC will also enjoy use of a new dedicated high-performance computing cluster starting this fall. You can officially apply for the position here: https://cuny.jobs/new-york-ny/research-associate-structural-biology-initiat… Feel free to contact Dr. Keedy directly at daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> with your CV and a brief description of your interests if you would like to discuss possible projects. Please pass this ad along to others who may be interested. Come join us in NYC! ~Daniel Keedy — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center www.keedylab.org<http://www.keedylab.org> | daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> | 212-413-3246

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Integrating Pymol and coot in Phenix
by Darin Lory 29 May '19

29 May '19

PhenixGurus, I'm trying to get pymol and coot to run as viewers in Phenix 1.15.2-3472-final. I have PyMol version 2.3.2 installed and coot 0.8.9.1 "coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python". I have the executables in the Linux path as per the FAQ. When I click on the coot button I get another window "Coot is being started with Phenix extentions pre-loaded. Depending on the computer speed, it may take several seconds for the program to open". I get this message: $ phenix Already checked for new versions in last 24 hours, skipping /apps/packages/phenix/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/start_coot.sh: line 37: /apps/packages/coot-installer/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/0-coot-history.py: No such file or directory Then I click on the PyMol button and get this: Could not import runpy module Traceback (most recent call last): File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module> import importlib.util File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module> from contextlib import contextmanager File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module> from collections import deque File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module> from reprlib import recursive_repr as _recursive_repr File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module> raise ImportError('This package should not be accessible on Python 3. ' ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted. $ which coot /apps/packages/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/coot $ which pymol /apps/packages/pymol/pymol $ which phenix /apps/packages/phenix/phenix-1.15.2-3472/build/bin/phenix My environment variables are: export PHENIX=/apps/packages/phenix export PHENIX_INSTALLER_DATE=080920070957 export PHENIX_VERSION=1.3 export PHENIX_RELEASE_TAG=final export PHENIX_ENVIRONMENT=1 export PHENIX_MTYPE=intel-linux-2.6-x86_64 export PHENIX_MVERSION=linux export PHENIX_USE_MTYPE=intel-linux-2.6-x86_64 source /apps/packages/phenix/phenix-1.15.2-3472/phenix_env.sh export PATH=${PATH}:${APPS_ROOT}/pymol:${APPS_ROOT}/pymol/bin:${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin:/usr/local/cuda-10.0/lib64:/usr/local/bin export LD_LIBRARY_PATH=${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/lib:/usr/local/lib64:/usr/local/lib:${APPS_ROOT}/cryoEF_v1.1.0/lib:/usr/local/relion3/lib:${LD_LIBRARY_PATH} KIndly advise, -Darin

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Can not decrease R-free value
by Pham, Hang 28 May '19

28 May '19

Dear all, I am refining my structures at 2.5 A. The model is well fitting in the electron density. I already add water and ligands. I’m trying these options (XYZ coordinates, real-space, TLS parameters, Individual B-factors, Optimize X-ray/stereochemistry weight, Optimize X-ray/ ADP weight, Reference model restraints, Use secondary structure restraints, Simulated annealing (Cartesian), Automatically correct N/Q/H errors) to refine the structure but the R-free still be high. The reference model is 98% identity with the structure that I’m building. After refining, the R-work always decrease while R-free increase. My last values for R-work is 0.2501 and for R-free is 0.3246. I’m lost and don’t know what to try more. Can anyone could explain me what happens here ? What others options that I could use to optimize R-free value ? Thank you in advance ! Hang Pham ------------------------------------------------------ Hang Pham, Ph.D Student, The Doucet Lab Centre Armand-Frappier Santé Biotechnologie Institut National de la Recherche Scientifique (INRS) Université du Québec Réseau International des Instituts Pasteur 531 Boulevard des Prairies Laval (Québec) H7V 1B7 CANADA Téléphone : (450) 687-5010, poste 4210 Site web: http://www.profs.inrs.ca/ndoucet/

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ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.
by Darin Lory 21 May '19

21 May '19

Phenix Gurus, I'm trying to setup PyMOL(TM) 2.3.2 with Phenix 1.15.2-3472. My pymol is installed in file /apps/packages/pymol/pymol /apps/packages/pymol/pymol: symbolic link to `bin/pymol' I setup in Phenix -> Preferences -> Graphics -> PyMol Path as /apps/packages/pymol/bin/pymol. Any ideas why this is happening? My source file is /apps/packages/phenix/phenix-1.15.2-3472/phenix_env.sh #!/bin/sh # export PHENIX="/apps/packages/phenix/phenix-1.15.2-3472" export PHENIX_VERSION=1.15.2-3472 . $PHENIX/build/setpaths.sh ++++++++++++++ ++++++++++++++ phenix Already checked for new versions in last 24 hours, skipping Could not import runpy module Traceback (most recent call last): File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module> import importlib.util File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module> from contextlib import contextmanager File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module> from collections import deque File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module> from reprlib import recursive_repr as _recursive_repr File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module> raise ImportError('This package should not be accessible on Python 3. ' ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted. Best regards, -Darin "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'" -Issac Asimov [image: --] Darin S. Lory [image: https://]about.me/darin.lory <https://about.me/darin.lory?promo=email_sig&utm_source=email_sig&utm_medium…>

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minimizing clash score
by Titus, Erron 18 May '19

18 May '19

Hello, In order to improve model geometry of my x-ray structure, I am using real-space refinement together with reciprocal space refinement in phenix.refine. I like this, because it works very well to fix a lot of geometry issues. But clashes are a problem. Clashes tend to keep coming back. I found a clunky way to selectively use reference restraints to prevent most of the clashes from coming back, but I am wondering if there is another way of addressing this. I don't want to up-weight geometry globally, because 1) there are major regions of the x-ray map that are quite good, and 2) I don't have problems with other geometry, just clashes. I couldn't find much documentation on the "clash_guard" keyword... Thanks. Erron

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Re: [phenixbb] minimizing clash score
by oleg＠quantumbioinc.com 17 May '19

17 May '19

Dear Erron, We recently demonstrated that the high clash count typically seen with the conventional PHENIX refinement is likely attributed to a particular non bonded restraint function used by phenix.refine. When we employed QM/MM (ONIOM) refinement (Borbulevych et al., Acta Cryst., 2018, D74, 1063 https://doi.org/10.1107/S2059798318012913 ) that resulted in significantly better clashscore and improvements of other metrics. QM/MM refinement is available within PHENIX with the DivCon plugin. This plugin is available at no cost to academic users at http://www.quantumbioinc.com/products/software_licensing. Sincerely, Oleg Borbulevych Oleg Borbulevych, Ph.D. Staff Scientist QuantumBio, Inc. 2790 W. College Ave. State College, PA 16801 E-mail: oborbulevych(a)yahoo.com, oleg(a)quantumbioinc.com Linkedin Professional Profile: https://www.linkedin.com/in/oleg-borbulevych-b8045422 -----Original Message----- From: "Titus, Erron" <Erron.Titus(a)ucsf.edu> Sent: Friday, May 17, 2019 1:58pm To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] minimizing clash score _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.orgHello, In order to improve model geometry of my x-ray structure, I am using real-space refinement together with reciprocal space refinement in phenix.refine. I like this, because it works very well to fix a lot of geometry issues. But clashes are a problem. Clashes tend to keep coming back. I found a clunky way to selectively use reference restraints to prevent most of the clashes from coming back, but I am wondering if there is another way of addressing this. I don't want to up-weight geometry globally, because 1) there are major regions of the x-ray map that are quite good, and 2) I don't have problems with other geometry, just clashes. I couldn't find much documentation on the "clash_guard" keyword... Thanks. Erron

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Dots and vectors of cryo em validation in Coot
by Ahmad Khalifa 17 May '19

17 May '19

Hello, In the manual, it says the red dots are clashes, what about the yellow dots and the magenta dashes (vectors)? I would also appreciate if you give an input on how you fix them. Best regards.

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On estimating Unitary Structure Factor distribution
by Andre LB Ambrosio 15 May '19

15 May '19

Dear all, We seek to calculate the distribution of Unitary Structure Factors, Uhkl, from a few datasets (at different maximum resolutions) for which the corresponding atomic models are already available at the PDB; this according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) Hence, the following questions: - Is there any macromolecular crystallography software that can compute Uhkl as above, or equivalent? - If not, would it be more correct to use the Wilson-B or the mean B from the final model? - How can F(000) be best estimated from the final model, which is not necessarily always the most complete or best refined? Should we simply add together the number of electrons for all the atoms refined in the asymmetric unit (protein + ligands + solvent)? Many thanks in advance and best wishes, -- Andre LB Ambrosio

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