- phenixbb - phenix-online.org

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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Postdoctoral Research Assistant at University of Dundee (Alessio Ciulli)
by KH Chan 15 May '19

15 May '19

Posting on behalf of Prof. Alessio Ciulli: Professor Alessio Ciulli’s laboratory is seeking a postdoctoral researcher to undertake research in collaboration with one of the leading pharmaceutical companies supporting the Division of Signal Transduction Therapy (DSTT). The DSTT facilitates collaborations between some of the world’s major pharmaceutical companies (Boehringer Ingelheim, GlaxoSmithKline, and Merck-Serono) and leading Dundee-based researchers with a proven track record of achievement in understanding and exploiting the fundamental molecular causes of human disease in the fields of cancer, immune-regulation, neurodegeneration and hypertension resulting from disruptions in protein ubiquitylation, phosphorylation and other signalling networks. The successful applicant will be based within the Ciulli lab in Dundee ( http://www.lifesci.dundee.ac.uk/groups/alessio-ciulli). The laboratory is pioneering novel chemical structural biology approaches to target E3 ubiquitin ligases with small molecules. The applicant will employ state of the art structural biology, cell biology and biophysical approaches to conduct molecular and structural studies on disease-relevant human E3 ubiquitin ligases. The Ciulli lab has close collaborations and access to facilities available within both the MRC Protein Phosphorylation Unit ( http://www.ppu.mrc.ac.uk/) and more widely within the School of Life Sciences. This set-up will ensure the successful candidate will have access to whatever technologies required to conduct the projects that they are working on, including molecular, biochemical, mass spec proteomics, pharmacological and genetic methodologies including CRISPR/CAS9 knock-out and knock-in technologies. There will be regular opportunity for interaction and to discuss data within the group and with the collaborating pharma company. Candidate requirements: ‧ PhD with outstanding academic track record and at least one first authored publication in an internationally recognised peer-reviewed journal. ‧ Strong background in Biochemistry, Molecular Cell Biology, or Structural Biology is required. ‧ Strong interest in signal transduction research and how disruptions of these pathways are linked to human disease is expected. ‧ Experience with recombinant protein expression and purification, molecular cloning, and protein X-ray crystallography (or cryo-EM) is required. ‧ Experience with mammalian cells tissue culture, and protein-protein interaction studies inside cells e.g. pull-down, proteomics, would be highly advantageous. ‧ Experience with biophysical methods to study in vitro protein-protein and protein-peptide interactions is desirable. ‧ Capable of working in a team, but able to plan and work independently. ‧ Excellent communication skills and knowledge of the English language are essential. ‧ The candidate should have ambitions to become a successful independent researcher either in academia or the pharmaceutical/biotechnology industry. The fund for this project is available till 30th June 2020 in the first instance with a chance to renew. For informal enquiries please contact Prof Alessio Ciulli a.ciulli(a)dundee.ac.uk or Dr Kwok-Ho Chan k.chan(a)dundee.ac.uk Closing Date 31 May 2019 Job details: https://ig5.i-grasp.com/fe/tpl_uod01.asp?newms=jj&id=103176&newlang=1

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Research Associate (Fixed Term) at the MRC Mitochondrial Biology Unit, University of Cambridge
by Jonathan Ruprecht 15 May '19

15 May '19

Posting on behalf of Dr Edmund Kunji: The University of Cambridge wishes to appoint a Postdoctoral scientist to join the research group of Dr Edmund Kunji in the MRC Mitochondrial Biology Unit of the University of Cambridge. The postholder will work within a programme focussed on mitochondrial transporters. Transport processes are crucial for the functioning of mitochondria and mutations in transport proteins cause of a wide range of metabolic, neuromuscular and developmental diseases. Basic molecular understanding of their structure and mechanism is required to understand their role in health and disease. The goal of the project is to study their structures in different conformational states by electron cryo-microscopy and/or x-ray crystallography. The post-holder will participate in every stage of the process, from the generation of expression strains or cell lines, isolation of mitochondria, purification and sample preparation, data acquisition and processing, and structure model building and interpretation. There will also be an opportunity to study their role and mechanism using a wide range of biochemical and biophysical techniques. This project is part of a collaborative SNF Sinergia grant together with Profs. Hediger and Lochner of the University of Bern. Candidates will have a PhD in Structural Biology/Biophysics or related disciplines, and a track record of research achievements. Knowledge of protein purification and experience in structural biology are essential. Further details about the job may be found here: http://www.jobs.cam.ac.uk/job/21519/ The MRC Mitochondrial Biology Unit is a world-renowned centre for mitochondrial research. Additional information can be found at www.mrc-mbu.cam.ac.uk. Fixed-term: The funds for this post are available for 3 years in the first instance. The closing date for applications is Wednesday 12th June 2019 with interview date yet to be confirmed. Informal enquiries may be made to Dr Edmund Kunji (ek(a)mrc-mbu.cam.ac.uk).

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Cutting out a fragment from cryoEM map
by Sunandan Mukherjee 14 May '19

14 May '19

Hi, I want to build an RNA model using cryo-EM density. The structure is of a protein-RNA complex and the map consists regions with protein subunits. Is it possible to separate the portion of the map which represents the RNA only? Thanks and regards, Sunandan -- Sunandan Mukherjee (PhD) Research Assistant Laboratory of Bioinformatics and Protein Engineering International Institute of Molecular and Cell Biology (IIMCB) ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

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Low resolution structure determination workshop at ECM32
by Paul Adams 13 May '19

13 May '19

Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the 32nd European Crystallographic Meeting in Vienna: Low resolution structure determination and refinement of biological macromolecules by crystallography and cryo-EM Organizers: Paul Adams, Dorothee Liebschner (Lawrence Berkeley Laboratory, Berkeley, USA) Date: 18th August 2019 Time: 9 a.m. – 5 p.m. More details: https://www.ecm2019.org/satellites/ Meeting and satellite registration: https://www.ecm2019.org/submission-registration/registration/online-registr… Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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AUC2019 – early bird registrations closing soon....
by Renwick Dobson 13 May '19

13 May '19

Dear AUC and Structural biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/. Early Bird Registrations close on 15th June. As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. The meeting is also timed such that delegates can also attend the Biomolecular interactions and Engineering Symposium<https://www.queenstownresearchweek.org/bio-interactions/>, which is part of the Queenstown Molecular Biology Conference (this is in Queenstown, NZ), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

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Electron microscopy software tools workshop at ACA
by Paul Adams 12 May '19

12 May '19

Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the American Crystallographic Associate meeting in Covington: Introduction to PHENIX for Electron Cryo-Microscopists Organizers: Paul Adams (Lawrence Berkeley Laboratory, Berkeley, USA) Date: Saturday, July 20, 2019 Time: 9 a.m. – 5 p.m. More details: https://www.aca2019mtg.com/workshops Meeting registration: https://www.aca2019mtg.com/registration Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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MR-Rosetta installation
by Taberman, Helena 09 May '19

09 May '19

Dear Phenix bb, I am facing a problem when trying to instal Rosetta locally. I have installed Rosetta 3.9, set a local environment to my c-shell (setenv PHENIX_ROSETTA_PATH "/Applications/rosetta_src_3.10_bundle") and compiled with ./scons.py -j4 mode=release bin in main/source/ folder. When I try to run rosetta.run_test I get the following error:"OSError: [Errno 2] No such file or directory: '/Applications/rosetta_src_3.10_bundle/main/source/bin' " though the folder is there. Could you please help me? Cheers, Helena -- Helena Taberman, PhD Postdoctoral Researcher Helmholtz-Zentrum Berlin for Materials and Energy Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 12489 Berlin, Germany Tel: +49 30 8062 14376 Email: helena.taberman(a)helmholtz-berlin.de<mailto:[email protected]> Web: http://www.helmholtz-berlin.de/bessy-mx ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin

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Rosetta cannot Rebuild
by Perry, Kay H. 09 May '19

09 May '19

I am having a problem with mr_rosetta where I cannot make it past the rebuild step. I have made fragment files using the old Robetta Server and I am using a hhpred alignment file, but even if I try with a model_already_placed when I reach rebuilding, I get the following error. protocols.looprelax: === protocols.looprelax: === Remodel protocols.looprelax: === ERROR: frag_libs().size() > 0 ERROR:: Exit from: src/protocols/comparative_modeling/LoopRelaxMover.cc line: 47 7 My PHENIX_ROSETTA_PATH is pointed at /share/apps/necat/programs/rosetta3.4 so I believe I am using version 3.4 of rosetta. Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692

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Fwd: NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago
by Yury Polikanov 08 May '19

08 May '19

NIH/NSF-Funded 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 positions 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/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). 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=113640&job=visiting-resear… by June 28, 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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phenix-1.15.2-3472 crashes with multiple CIF's
by oleg＠quantumbioinc.com 03 May '19

03 May '19

phenix-1.15.2-3472 crashes at the very end of the refinement when multiple CIF's are given at the command line (see below). Please have a look. Thanks 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 ============================== Exporting results ============================== Writing refined structure to PDB file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.pdb n_use = 9639 n_use_u_iso = 9639 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 9639 Writing refined structure to CIF file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.cif Traceback (most recent call last): File "/home/oleg/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 162, in run refine_object.write_model_cif_file(f_cif_model) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 984, in write_model_cif_file additional_blocks=[cif_block]) File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 964, in model_as_mmcif restraints = self.extract_restraints_as_cif_blocks() File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 862, in extract_restraints_as_cif_blocks if '_chem_comp_plane_atom.comp_id' in loop.keys(): AttributeError: 'NoneType' object has no attribute 'keys'

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 02 May '19

02 May '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the July 2019 issue is 20 May 2019. The previous issue is available http://phenix-online.org/newsletter/ and contains the following. January 2019 <http://phenix-online.org/newsletter/CCN_2019_01.pdf> Short Communications - MARCO: The Machine Recognition of Crystallization Outcomes <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=7> - Building a model the way you do: Map-to-model version 2 <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=9> Fitting tips #16 – Asn and Gln are remarkably different <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=1> FAQ - Are the defaults the best for refinements? <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=6> 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel 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

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geometry_restraints.edits.scale_restraints
by Wei Wang 02 May '19

02 May '19

Dear PHENIX developers, I would like to know if the refinement.geometry_restraints.edits.scale_restraints still a valid option for tightening local restraints. I didn’t see this option from the phenix —show-defaults=all. I saw this option on the FAQ webpage. thx Wei

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Phaser Small Molecule MR
by Whitley, Matthew J 02 May '19

02 May '19

Hello all, We have collected electron diffraction data to approximately 1.8 Å on a 'small molecule' of roughly 1660 Da. The space group (P 43 21 2) and unit cell parameters determined during data reduction match the known, published values, and our data are roughly 80% complete in all resolution shells from 17 - 1.8 Å. We would like to solve this structure by molecular replacement in Phaser, but are having a bit of difficulty doing so. Our problems all seem to be related to specifying the composition of the target molecule for Phaser. Via the phenix GUI, we can only specify the target composition as either protein or nucleic acid, when in fact the target is neither. The chemical composition of the target is C72 H85 N19 O18 S5. Is there a way to feed this chemical composition to Phaser and to get it to understand that the target is neither protein nor nucleic acid? Furthermore, according to our reading of the Phaser documentation, specifying "protein" leads to an assumed solvent content of 50%, which is likely to be a substantial overestimation for this small molecule crystal. We have also run into the problem of Phaser complaining that the target molecule will not fit into the given unit cell, which we think is due to the assumption of 50% solvent content. We would be thankful for whatever advice you may have on using Phaser with non-protein, non-nucleic acid molecules. Matthew --- Matthew J. Whitley, Ph.D. Research Instructor W. Furey Lab Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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Phenix elbow unable to determine bonding
by Ahmad Khalifa 01 May '19

01 May '19

I'm not sure why I'm getting this error. I generated restraint files for GDP with no problems. I noticed that if I change the coordinates of my files, I have to regenerate a new restraint files to match the new coordinates. This time I'm getting this error that I couldn't troubleshoot: Please find attached my gdp.pdb. --------- ['/storage/IJ/.phenix/project_data/elbow_88.eff'] --------- <function run at 0x7fbd2b4bb938> Working parameter elbow { input { chemical_file_name = None chemical_file_name_type = *auto pickle chemical_string = None chemical_string_type = *smiles sequence geometry_file_name = /storage/00_Marina_Ahmad/Tubulin/real_space_refinement/GDP.pdb geometry_file_name_usage = *topology initial orientation final assist template_file_name = None chemical_components_code = None residue = None read_only = False do_all = False optimisation_choice = None *auto am1 mogul ampac gamess gaussian jaguar \ mopac nwchem orca qchem } defaults { id = """GDP""" name = None pH = low *neutral high random_seed = None add_hydrogens = None write_hydrogens = True write_redundant_dihedrals = False multiple_planes = False auto_bond_cutoff = 1.95 pdb_attributes { resseq = 1 icode = None chain_id = A } } optimisation { steps = None tolerence = loose *default tight memory = 1000Mb energy_validation = None third_party_apps { nprocs = 1 method = *uhf mp2 b3lyp basis = *am1 sto-3g 3-21g 6-31g 6-31g(d) 6-31g(d,p) aux_basis = None } } view { view_results = *None reel molden pymol } output { no_output = False output = None output_dir = /storage/00_Marina_Ahmad/Tubulin/real_space_refinement/ pass_through_input_restraints = None pass_through_library_restraints = None output_file_formats = *pdb *cif pdb_ligand tripos sdf data_sheet png xyz \ maestro data_header_file = "" job_title = """GDP""" overwrite = False console_output = *default quiet silent chiral = *retain both enumerate pucker = *random enumerate define pucker_definition = "" cis_trans = *retain enumerate png = False } special { regno = None secondary_smiles = None amgen_id = None } non_user_parameters { opt_type = simple input_type = pdb_rich use_template = False } } ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.14-3260 None - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Option opt_type not available Option input_type not available Option job_title not available Option use_template not available Random number seed: 3628800 Initial processing time : 0.00 seconds 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P Input format is PDB MoleculeClass : C:10 N: 5 O:11 P: 2 (PDB format) 28 atoms 30 bonds 0 angles 0 dihedrals 0 rings 0 chirals Predicted memory usage by semi-empirical method : 45Mb Timing estimates Python portion / ATP : 86% c++ optimisation cycle / ATP : 76% 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise B Failed to determine the bonding of a fragment of the molecule. PDB file elbow.GDP.GDP_pdb.001.pdb written. Bonding file elbow.GDP.GDP_pdb.001.bonding.py written. Edit bonding file to reflect the desired bond. ALTERNATIVELY Re-run eLBOW with the --reel option and the molecule wil be loaded into REEL. Edit the bonds and save the results as "fixed.cif" to allow eLBOW to load the bonding. You can also use a pull-down menu to push to eLBOW.

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NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago
by Yury Polikanov 01 May '19

01 May '19

NIH/NSF-Funded 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 positions 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/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). 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=113640&job=visiting-resear… by June 28, 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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modelling into positive densities
by Sam Tang 29 Apr '19

29 Apr '19

Hello, I am refining a structure solved to 1.5A by MR. Rw/Rf were 0.17/0.22 which seem acceptable to me. At the very beginning part of the protein the electron density is a bit wobbly. I am able to build the residues into the positive densities. But after phenix.refine the chain always shifts away a bit and leaves the green blobs there. (Photo: https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R) I am thinking if this can be solved by adjusting the target weights. Or can I apply certain restraints only to those few residues? I refined XYZ (reciprocal space), XYZ (real space), individual B-factors, TLS and occupancies. Thanks in advance. Regards Sam

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molprobity vs validation_cryoem
by Roberto Marabini 28 Apr '19

28 Apr '19

Hi guys, We are using phenix version 1.15.2-3472. We have executed molprobity using the command line: phenix.python_1.15.2-3472 /usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/command_line/molprobity.py "path_to_pdb"/refmac-refined.pdb pickle=True nproc=4 We have also executed validation_cryoem (here we have used both the GUI and the command line and both interfaces return the same result) phenix.python_1.15.2-3472 ./phenix/phenix/command_line/validation_cryoem.py "path_to_pdb"/refmac-refined.pdb "path_to_map"/molprobity.mrc resolution=3.2 pickle=True What we do not fully understand is why the two commands return different results for molprobity. Are the default parameters different? For example, validation_cryoem reports as number of outliers "34" in the molprobity tab (model.geometry.angle.outliers) while molprobity reports 21 The test files are available at: 3Dmap: https://drive.google.com/open?id=0B_i_LJfUN1z7amoyM1B2N1U0Y2VYODB6LWdLY1pwa… pdb file: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093775/ Thanks for the help

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