- phenixbb - phenix-online.org

New bug in phenix.refine
by Aaron Oakley 23 Jun '19

23 Jun '19

Phenix.refine used to be able to handle a ligand covalently bound to cysteine if an appropriate cif dictionary was provided. This now seems to be broken. Re-running a job that used to work now fails. KeyError : 'link_CYS-MPS' Traceback: File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 180, in run return_value = self.target() File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 75, in __call__ result = self.run() File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 79, in run refine_object = self._run(args, callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 92, in _run call_back_handler=callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 224, in __init__ run_clash_guard=False) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 1124, in setup_restraints_manager assume_hydrogens_all_missing = not self.has_hd()) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5509, in geometry_restraints_manager log=self.log) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5154, in construct_geometry_restraints_manager log=log, File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 751, in process_nonbonded_for_links origin_id = origin_ids['link_%s' % key] File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py", line 35, in __getitem__ raise e

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Refining alternate conformation of duplex DNA
by ABHISHEK SUMAN 20 Jun '19

20 Jun '19

Hello All, I am solving a X-ray crystal structure of protein-DNA complex at 2.3 Angs. In my structure, it seems like the the duplex DNA is bound in two different conformations, and both the conformations are occupied in same density. I wish to know how to refine the alternative conformations of the DNA duplex in Phenix. In am using Phenix GUI. Thanks Abhishek *______________________________________________* *Abhishek Suman* *Research Scholar, PhD* C/o, Dr. Rajakumara Eerappa Macromolecular Structural Biology Group Department of Biotechnology R# 517,315, Academic Block - A Indian Institute of Technology Hyderabad Kandi 502 285 Sangareddy Telangana INDIA Contact: +91 91002 74548 (O) +91 80843 11898 (R) Email: abhisheks.iith(a)gmail.com ----------------------------------------------------------------- *Please don't print this e-mail or attachment unless necessary. Preserve trees on the planet.*

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ISOLDE 1.0b3 release
by Tristan Croll 17 Jun '19

17 Jun '19

Dear structural biology community members, I am happy to announce that ISOLDE 1.0b3 is now live and available for installation via the ChimeraX Tool Shed. To get it, just download, install and run the ChimeraX 0.9 release version from http://preview.cgl.ucsf.edu/chimerax/download.html#release, then go to Tools/More tools… and find ISOLDE in the web page that appears. If you’re unfamiliar with what ISOLDE is about, in brief it’s an interactive model-building environment specifically tailored for the challenges encountered in fitting low-medium resolution maps. Find out more at https://isolde.cimr.cam.ac.uk. Best regards, Tristan What’s new in 1.0b3: - parallelised structure factor calculations (courtesy of ISOLDE’s sister plugin, ChimeraX_Clipper). - support for a wider range of chemical space (glycosylations courtesy of GLYCAM and various other post-translational modifications, and ~13,000 of the more common ligands in the wwPDB thanks to the work of Nigel Moriarty and David Case) - adaptive distance restraints (for reference model restraints and/or large-scale interactive flexible fitting – see https://isolde.cimr.cam.ac.uk/features-main/interactive-restraints/). - ability to fetch model and structure factors (as F/sigF, I/sigI or anomalous equivalents) straight from the wwPDB - interactive tutorials (run the command “isolde tut” on the ChimeraX command line) - various general usability and performance improvements.

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NIH/NSF-Funded Visiting Research Specialist Position at the University of Illinois at Chicago
by Yury Polikanov 17 Jun '19

17 Jun '19

NIH/NSF-Funded Visiting Research Specialist Position in Structural Biology at the University of Illinois at Chicago The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for talented, skillful, and highly motivated researchers to fill the NIH/NSF-funded Visiting Research Specialist position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury .polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.…>) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov <https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbios.uic.…>). The successful candidate will be involved in determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography techniques. Basic qualifications: • BS degree in chemistry, biochemistry, biophysics, or a related field is required; • MS degree or higher is preferred;• Minimum of 3 years of laboratory research experience is required; • Strong background in biochemistry and molecular biology is required; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is not required but is highly desirable; • Experience in RNA biology field is not required but is highly desirable; The successful candidate is also expected to: • Act independently in terms of planning and executing the experiments; • Compile, analyze, and prepare data for publications; • Assist with training of graduate and undergraduate students. Interested candidates should submit their CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=115527 <http://email.hiretouch.com/wf/click?upn=JvIYOHR1NyNpkeKMwd5M2xA-2FeX5NPtxOr…> by July 1, 2019. Cover letter should be describing how previous research accomplishments and scientific interests of a candidate fit with the scope of the research in the Polikanov Lab. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act *Jacquelyn DeLaurentis* *Human Resource Associate* *Department of Biological Sciences* *The University of Illinois at Chicago* *845 W Taylor St. * *3238 SES, MC 066* *Chicago, IL 60607* *(312) 996-2213* *jdelaur(a)uic.edu <jdelaur(a)uic.edu>* [image: UIC Logo]

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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 08 Jun '19

08 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 30 May '19

30 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 29 May '19

29 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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