- phenixbb - phenix-online.org

Raw diffraction images for SARS-CoV-2 related structures
by Gerard Bricogne 18 Mar '20

18 Mar '20

Dear colleagues, Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease structures in the PDB seems to indicate that that there might be potential to improve these if refinements could be repeated after some reprocessing and further analysis of the raw diffraction images, rather than against the deposited merged data. This statement should in no way be construed as a criticism of the remarkable achievements of the research groups concerned, who have been operating under tremendous time pressure, but as an exciting opportunity to push methods to their limits on a uniquely significant class of structures. Another consideration is that the various logistical problems created by COVID-19 may soon make it increasingly difficult to collect new diffraction data on potential drug targets relevant to the fight against SARS-CoV-2, underlining the importance of ensuring that the best results be obtained from every dataset actually collected, and that the most useful conclusions be drawn from the analysis of those datasets towards improving the quality of subsequent data collections. On this basis we would like to propose that special efforts be made to grant public access to the raw image data associated with any SARS-CoV-2 related structure that is deposited into the PDB. This can be done by (1) archiving these raw image data using resources such as data.sbgrid.org, zenodo.org, proteindiffraction.org or any other cloud-based data-sharing service, and (2) communicating the corresponding DOIs to the wwPDB centres. This idea could be extended to datasets that investigators would like to offer to interested methods developers or expert users at the pre-deposition stage. Experts making use of those raw data would be encouraged to document, in as much detail as possible, how particular programs or workflows could be used on those structures/datasets to obtain the best results. This would be a kind of "virtual workshop", a particularly valuable collective activity at the present time when several in-person workshops (e.g. RapiData) have been cancelled and many meetings are in limbo for several months. The latter activity would benefit from having a centralised facility set up for the experts to post their results and annotations: we could create such a facility, but other, larger groups might want to consider doing so. With best wishes, Clemens & Gerard.

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Transferring Phenix home
by csteussy 18 Mar '20

18 Mar '20

All, In this age of self quarantine I have moved a number of my PHENIX projects home. All the working subdirectories have a .phenix entry. Is there a way to incorporate the history of the projects from work to my home installation. Starting the GUI shows none of it. Both of these are Ubuntu 18.04 and I have sudo privileges. Thanks in advance. Nic out

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COVID-19 Structural Biology Data Analysis
by Paul Adams 18 Mar '20

18 Mar '20

Dear Colleagues, with the effects of COVID-19 being felt worldwide, we all want to do something to help. There are several teams that are using crystallography and cryo-EM to help develop diagnostics and therapeutics for the virus. We wanted to let you know that the members of the Phenix team stand ready to assist with the analysis of COVID-19 related data should that be helpful to you. Please feel free to contact any of us. We hope that you are able to stay safe in this very challenging time. Paul, on behalf of the Phenix Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. [repost]
by Bjørn Panyella Pedersen 18 Mar '20

18 Mar '20

Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://tiny.cc/MBG_postdoc We are looking for a highly skilled and motivated postdoc with an interest in working on sugar transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2020, but starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. Deadline: All applications must be made online (http://tiny.cc/MBG_postdoc) and received by 2. apr. 2020.

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Slurm/qsub queue usage
by Michael Weyand 18 Mar '20

18 Mar '20

Dear Phenixer, I would like to use Phenix GUI queue execution option. We have access to cluster nodes via Slurm/qsub. https://slurm.schedmd.com/documentation.html The reason is that we have severe problems to run Coot/PyMol form the Phenix GUI if Phenix is executed on our number cruncher. This direct Coot usage GUI option is HIGHLY preferred by my young colleagues... Therefore my Slurm queue installation. But I have no clue how to add the needed first qsub script line ( "#!/bin/bash" or "#!/bin/tcsh" ) to the final Phenix command script from the Phenix GUI, which is to my knowledge a must for the qsub/sbatch command. Same holds true for the CCP4i GUI ... :-( This line is added to avoid cross positing to CCP4BB ... ;-) Is there any simple hint / command which I have missed ? Kind regards, Michael

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exit code 126
by Wim Burmeister 18 Mar '20

18 Mar '20

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crash when running PDB Tools job in 1.18rc4
by Daniel Larsson 18 Mar '20

18 Mar '20

Just want to report a bug in the latest release candidate. I just installed it and when I try to open an old PDB Tools job or start a new one, the GUI crashes without any error message. The same thing works fine with 1.18rc1. I’m using macOS 10.14.6 (Mojave). Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Fwd: prepare_pdb_deposition produce incomplete results in version 1.17
by Billy Poon 13 Mar '20

13 Mar '20

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Wed, Mar 11, 2020 at 11:51 PM Subject: Re: [phenixbb] prepare_pdb_deposition produce incomplete results in version 1.17 To: Marta Martinez <mmmtnez(a)cnb.csic.es> Hi Marta, The mmCIF functionality is very much still a work in progress as we try to make the process more robust. The ? in the column from 1.17 is a consequence of some changes we had made to the code and we're working on fixing that. The secondary structure issue with Chimera is separate since that column is for matching the protein chain with the sequence, not as a way to annotate secondary structure. We are working with the wwPDB to make sure our output is in compliance with the latest mmCIF dictionary. Let us know if you have any other questions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Mon, Mar 9, 2020 at 10:05 AM Marta Martinez <mmmtnez(a)cnb.csic.es> wrote: > > Hi, > > In the past (phenix version 1.13) we have been using > prepare_pdb_deposition to generate CIF files of atomic structures. In > the last version (1.17) the program produces an incomplete output if > the input is a PDB file. > > The tests have been carried out with the protein hemoglobin (PDB > ID = 5ni1). If we downloaded it from the PDB databank we get the file > 5ni1.cif. If we "export" 5ci1.cif using prepare_pdb_deposition the > result is correct. On the other hand, if we convert 5ci1.cif to PDB > either using chimera uscf or maxit > (https://sw-tools.rcsb.org/apps/MAXIT/index.html) and then we execute > prepare_pdb_deposition, one of the columns (label name = > _atom_site.label_entity_id) is filled with the symbol "?" instead of > the label_entity_id (as the version 1.13 did). One of the effects of > this misbehavior is that chimera displays the file as a set of > aminoacids with no connection between them (no secondary structure is > shown) > > > > A few lines of the file obtained using phenix 1.17: > > ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A ? > 1 1 > ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A > ? 1 1 > ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A ? > 1 1 > > Corresponding lines of the equivalent file obtained using phenix 1.13 > > ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A 1 > 1 1 > ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A > 1 1 1 > ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A 1 > 1 1 > > Note the difference in the ante-penultimate column. > > We would appreciate if phenix 1.17 is modified so the column > _atom_site.label_entity_id is filled with the proper chain ID. > > best wishes > > -- > Marta Martinez Gonzalez > > Biocomputing Unit (Lab B13) > National Center for Biotechnology-CSIC > Darwin, 3. Campus de la Universidad Autonoma de Madrid > 28049 Madrid. Spain > Tel:+34 915854510 Fax:+34 913720112 > E-mail: mmmtnez(a)cnb.csic.es > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org >

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phenix.geometry_minimization with amber option
by Wei Wang 12 Mar '20

12 Mar '20

Dear all, I try to use phenix.geometry_minimization with amber option, but when reaching minimization step, the function always crash. If I don’t use amber option, then it’s ok. The commands I put in was like: phenix.geometry_minimization 4phenix_xyz.pdb amber.use_amber=true amber.topology_file_name=4amber_xyz.prmtop amber.coordinate_file_name=4amber_xyz.rst7 amber.order_file_name=4amber_xyz.order I tried both 1.17 stable and latest overnight build. Please share your advice, thx! Wei

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prepare_pdb_deposition produce incomplete results in version 1.17
by Marta Martinez 09 Mar '20

09 Mar '20

Hi, In the past (phenix version 1.13) we have been using prepare_pdb_deposition to generate CIF files of atomic structures. In the last version (1.17) the program produces an incomplete output if the input is a PDB file. The tests have been carried out with the protein hemoglobin (PDB ID = 5ni1). If we downloaded it from the PDB databank we get the file 5ni1.cif. If we "export" 5ci1.cif using prepare_pdb_deposition the result is correct. On the other hand, if we convert 5ci1.cif to PDB either using chimera uscf or maxit (https://sw-tools.rcsb.org/apps/MAXIT/index.html) and then we execute prepare_pdb_deposition, one of the columns (label name = _atom_site.label_entity_id) is filled with the symbol "?" instead of the label_entity_id (as the version 1.13 did). One of the effects of this misbehavior is that chimera displays the file as a set of aminoacids with no connection between them (no secondary structure is shown) A few lines of the file obtained using phenix 1.17: ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A ? 1 1 ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A ? 1 1 ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A ? 1 1 Corresponding lines of the equivalent file obtained using phenix 1.13 ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A 1 1 1 ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A 1 1 1 ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A 1 1 1 Note the difference in the ante-penultimate column. We would appreciate if phenix 1.17 is modified so the column _atom_site.label_entity_id is filled with the proper chain ID. best wishes -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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