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intensity merging statistics for wwpdb deposition
by wtempel 03 Jul '19

03 Jul '19

Dear PHENIX users, how does one add merging statistics to PHENIX mmcif coordinates for deposition, assuming availability of AIMLESS logs and pre-merge intensities? Is this functionality implemented in PHENIX or CCTBX? Thanks. Wolfram Tempel

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r_work and r_free from an .mtz file containing Fobs and Fcalc
by Andre LB Ambrosio 01 Jul '19

01 Jul '19

Dear colleagues, Can Phenix calculate r_work and r_free from a .mtz file containing FP and FC_ALL (from PDB_REDO), without inputing the matching .pdb file? Many thanks in advance, -- Andre LB Ambrosio

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6th International Symposium on Diffraction Structural Biology: First Announcement
by Leighton Coates 01 Jul '19

01 Jul '19

Dear Colleague You are invited to the 6th International Symposium on Diffraction Structural Biology which will take place at the University of Osaka in Japan. Start Date: 17th Oct 2019 End Date: 20th Oct 2019 URL: https://isdsb2019.symposium-hp.jp/ The 6th International Symposium on Diffraction Structural Biology (ISDSB2019) is an international symposium organized by the Japan Society for the Promotion of Science, University-Industry Research Cooperative Research Committee, 169th Committee on Structural Biology using Diffraction Techniques. This symposium is positioned as an interface between academic researchers and industry researchers, as well as an interface between diffraction techniques and other related techniques in the field of structural biology. Symposium topics will include Macromolecular crystallography, CryoEM, software and databases, and drug discovery, registration and abstract submission for the symposium is now open and costs 25,000 Japanese yen for academics. A list of confirmed speakers for the symposium is currently being finalized; this will be posted on the symposium website within the next few days. Contact: Atsushi Nakagawa (Osaka University) Email: isdsb2019(a)gmail.com URL: https://isdsb2019.symposium-hp.jp/

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Mandatory PDBx/mmCIF format for crystallographic PDB depositions
by John Berrisford 01 Jul '19

01 Jul '19

>From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract <http://pdb-extract.wwpdb.org/> and MAXIT <http://sw-tools.rcsb.org/apps/MAXIT/index.html> . More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website <https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> . For more information, view the full news release at the wwPDB website <https://www.wwpdb.org/news/news?year=2019#5d17c1ceea7d0653b99c87e2> or contact the wwPDB on deposit-help(a)mail.wwpdb.org <mailto:[email protected]> . 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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PEG as a polymer
by Felix Cat 29 Jun '19

29 Jun '19

Hi all, I'm working on a structure where I see extensive interaction of the protein with PEG (polyethylene glycol). The largest PEGs I can find in structures in the PDB with a quick search are around 12 EDO subunits long, and they're called "dodecaethanediol" or the like. I am seeing at least 20. Currently, I've built the PEG as a giant, single ligand, and generated a viable cif file for it using eLBOW with a SMILES string (very simple for PEG, you can imagine). I'm wondering if I might rather be able to handle it as a polymer of EDO subunits. I started to dig into that but got lost pretty quickly. I can't figure out how to create an automatically link-able EDO molecule, all with proper geometry, and I don't want to have to tell phenix.refine about 19+ custom linkages every time. (I've had to do that with N-linked acetylglucosamine moieties in the past.) Nate NUNC

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Real space refinement with helical symmetry
by Yangqi Gu 29 Jun '19

29 Jun '19

Hi all, I am trying to do a real space refinement with phenix and my map is a filament and I have monomer model and I would like to refine against my filament map. I am wondering how to impose the helical symmetry in this case? (I have a pseudo filament model by copying multiple subunits and aligned in Chimera using "fit in map"). Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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CaBLAM fixing and interpretation in comprehensive validation for cryo-EM
by Ahmad Khalifa 28 Jun '19

28 Jun '19

Hello, I would appreciate some insights on how to interpret the validation results under the CaBLAM tab and how to use it to fix my structure in Coot? What are the CaBLAM score, the Ca geometry score, the helix score and the 3-10 score? How to use the information under the secondary structure tab? In my protein for example, I see a lot of "try beta sheets", should I try to refine that segment using beta sheets restraints? Best regards.

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(no subject)
by Pu Qian 28 Jun '19

28 Jun '19

Hi All I have a problem to do refinement for one of our cryo-em model caused by ligand of spirilloxanthin (wwPDB code CRT). I'm using phenix cryo-EM real-space refinement for one of my cryo-em models which contains a ligand called spirilloxanthin, a very common carotenoid molecule found in nature. Its code is CRT which can be found in wwPDB ligand dictionary and in COOT. However, when I run real-space refinement, I got a error message caused by this ligand "Fatal problem interpreting model file: Number of atoms with unknot non bonded type symbols: xxx please edit the model file to resolve the problem and /or supply a cis file with matching restrain definitions, along with apply_cif_modification and apply-cis-link parameter definitions if necessary". I checked my pdb file. All atom names and order are exactly same as that in wwPDB. I also try to insert it into map using COOT monomer find method. It does not work as well. It seems to me that Phenix can not recognise this ligand, CRT spirilloxanthin. Does anyone have an idea of how to deal with this issue. Or is it OK if I add CRT.cif into upload window of Phenix for refinement? Any suggestion is greatly appreciated. The version of Phenix I am using is Mac version recently downloaded from Phenix website. Best regards

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Position Opening: Synchrotron Macromolecular Crystallographer @ IMCA-CAT
by Lisa J. Keefe 28 Jun '19

28 Jun '19

Dear Colleagues, POSITION: Synchrotron Macromolecular Crystallographer LOCATION: IMCA-CAT at the Advanced Photon Source (near Chicago, IL) The Industrial Macromolecular Crystallography Association - Collaborative Access Team (IMCA-CAT) and the Hauptman-Woodward Medical Research Institute (HWI) seek an inventive macromolecular crystallographer to join the IMCA-CAT team in accelerating pharmaceutical drug discovery through synchrotron-based structural biology research. As an employee of HWI, you will be based at the center of the team’s operations at the Advanced Photon Source (APS), Argonne National Laboratory, near Chicago, IL. This is an ideal position for a motivated scientist who is passionate about delivering strategic value, developing new technologies, and working in a high- powered, collaborative environment. DESCRIPTION: This is an exciting time to join IMCA-CAT. Underway this summer is the first of a two-phase upgrade that will significantly increase throughput and establish a strong foundation upon which to build capacity. The second phase upgrade, currently in design, will profoundly increase capacity and dramatically expand capability for challenging research projects. The successful candidate will be an integral part of these upgrade activities while maintaining flow of diffraction data for pharmaceutical research projects. The candidate will work closely with IMCA-CAT colleagues in an inclusive and respectful environment, and is expected to take initiative and contribute to the team effort. On any given day, you will do one or all of these things: • Contribute to drug discovery research efforts using a growing portfolio of synchrotron sources. • Enhance the structural biology programs for pharmaceutical structure-based drug design. • Provide experiment support for scientists from the structural biology community who conduct research using the IMCA-CAT synchrotron beamlines. • Ensure beamline instrumentation is operational and produces data of the highest quality. • Expand the experiment envelope of the beamline. • Establish efficient protocols for accelerating data acquisition while enhancing data security. • Develop automated methods for acquiring quality data from challenging samples. • Participate in highly collaborative working groups. • Engage in the technical development of new strategies for ultra-high throughput. • Collaborate with staff on strategically-aligned research and development projects. • Communicate with researchers and present at meetings. • Conduct independent and/or collaborative research. DESIRED SKILLS and EXPERIENCE: • PhD in a relevant field. • Expertise in macromolecular crystallography. • Outstanding experimental skills. • Considerable mechanical skills. • Highly collaborative and team-oriented approach to conducting work and solving problems. • Excellent written and oral communication skills. • Deeply proactive approach to meeting and exceeding goals. • Ability to meet requirements for site access to Argonne National Laboratory. TO APPLY: Send an introductory email, cv, and contact information for three references to Lisa Keefe, IMCA-CAT Director and HWI Vice President of Advancing Therapeutics, at keefe(a)imca-cat.org. LEARN MORE: Visit our websites to learn more about IMCA-CAT (www.imca-cat.org) and HWI (www.hwi.buffalo.edu). HWI is an equal opportunity employer. Lisa J Keefe, PhD Director IMCA-CAT <http://www.imca-cat.org/> Industrial Macromolecular Crystallography Association - Collaborative Access Team 630.252.0544 • Sector 17 @ Advanced Photon Source, Argonne National Laboratory Vice President for Advancing Therapeutics Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/> Past-President American Crystallographic Association <http://www.amercrystalassn.org/> .

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Copying mtz file
by Cygler, Miroslaw 25 Jun '19

25 Jun '19

Hi Phenixers, I have copied mtz file to a new file with a lower resolution limit using the "Reflection file editor” tool. I copied all arrays to the output file. When I attempted to continue refinement with the new mtz file, a message appears saying that there are no R-free flags in the mtz file. Yet, the new file contains the R-free-flags column but the values are inverted, 1 is changed to 0 and 0 is changed to 1. In the output option dialog the box “Preserve original flag values” was checked. How to fix this? Thanks, Mirek

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Why the correlation coefficient of the electron density with the model is never 1?
by Murpholino Peligro 24 Jun '19

24 Jun '19

The links below show a plot of the results of phenix.real_space_correlation* for a nice lisozyme crystal and also the coot view. https://drive.google.com/open?id=0B9tqXyDsq9YIdkRhcVFXU2dEdnhINXR6Y3hza2Y5N… https://drive.google.com/open?id=0B9tqXyDsq9YIREd1OFZhNGZtRnN4aldtVU1mdk84N… As you can see the electron density fits very well the model. Why not a single residue gets a perfect correlation coefficient? (i.e. 1) Just curious. Thanks * phenix.real_space_correlation pdbfile mtzfile --detail="residue" > outpu

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New bug in phenix.refine
by Aaron Oakley 22 Jun '19

22 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 19 Jun '19

19 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 16 Jun '19

16 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 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 20 May '19

20 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 17 May '19

17 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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