- phenixbb - phenix-online.org

high level python API
by wtempel 07 Jul '18

07 Jul '18

Hi, I would like to call programs like phenix.refine from a python script. Is the python subprocess module my best bet? Or does phenix provide its own interface similar to, say, ccp4 dispatchers? Thanks. Wolfram Tempel

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 07 Jul '18

07 Jul '18

Hi Luc, No worries, let us know of any other concerns. 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 Fri, Jul 6, 2018 at 2:22 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > Or do you need something sooner? > > No, considering the timeframe for the move to conda is before the end of > the year. I just wanted to know so that I can start advertising the change > to the people on my side. Sorry if I missed that point during the meeting > you invited me on. > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Invitation to International conference "BIOMEMBRANES 2018"
by Marin, Egor 06 Jul '18

06 Jul '18

Fellow structural biologists, we are pleased to invite you to participate in the 4th biannual international C*onference* “BIOMEMBRANES 2018”, which will be held on October 1-5, 2018 at the Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia. This is the first meeting within the International Conference Series “Virtual Human – Imaging Across Scales” co-organized by scientists from Russia, Germany, China, and USA. Our speakers will focus on cutting-edge problems of modern integrative structural biology of biomembranes and membrane proteins, theoretical biophysics of membrane systems and computer modelling. The conference will highlight the role of biomembranes in aging and age-related diseases such as cancer, neurodegenerative (Alzheimer’s, Parkinson’s) and cardiovascular diseases. The talks will be given by world-leading scientists from Russia, USA, Germany, France, the Netherlands, China, Spain, Italy, Sweden and Switzerland. Preliminary scientific program, as well as the up-to-date list of speakers please find here: https://biomembranes2018.ru/program/ In parallel, an international *School* “Mechanisms of aging and age-related diseases” will take place as a satellite event of the Conference on September 30 - October 5, 2018. The full information about the school will soon be available on our web-site https://biomembranes2018.ru/sa tellite-events. Early bird registration until 31.07, registration until 14.09. Further information is available on the conference web site http://biomembranes2018.ru. We are looking forward to meet you in Dolgoprudny! sincerely yours, Organizing Committee

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Re: [phenixbb] [cctbxbb] Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 06 Jul '18

06 Jul '18

Hi Luc, With the planned migration to conda for dependencies, the idea is to build one linux installer using the compilers in conda (currently GCC 7.2, https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html) and then test that installer on multiple distributions of linux. CentOS 7 would be one of the distributions used for testing. Or do you need something sooner? We currently do not build our installers on CentOS 7, but I have checked that the CentOS 6 installer runs and that the regression tests (phenix_regression.test_all_parallel, which is a superset of cctbx regression tests) pass on CentOS 7. -- 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 Wed, Jul 4, 2018 at 7:31 AM Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > Hi Billy, > > > The upcoming Phenix 1.14 official release will still have installers for > CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting > CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life > Cycle Support Add-On (until November 30, 2020), we are planning on > deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are > planning on deprecating 32-bit support for Windows because only a few > percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are > for 32-bit versions. > > > If you deprecate CentOS 5, will you start to support CentOS 7? I mean > right now, nightly tests run CentOS 5 & 6. Do you plan to make it 6 & 7? I > am asking so that I can start planning for Bruker among other things… > > Best wishes, > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Deprecating legacy support (CentOS 5, Windows 32-bit) in CCTBX and Phenix
by Billy Poon 03 Jul '18

03 Jul '18

Hi everyone, The upcoming Phenix 1.14 official release will still have installers for CentOS 5 and Windows 32-bit, but since CentOS is no longer supporting CentOS 5, and RedHat is only supporting RHEL5 through their Extended Life Cycle Support Add-On (until November 30, 2020), we are planning on deprecating CentOS 5 support (32-bit and 64-bit). In addition, we are planning on deprecating 32-bit support for Windows because only a few percent (< 5% for both Windows and CentOS 5) of our Phenix downloads are for 32-bit versions. Please let us know if support for CentOS 5 (32-bit and/or 64-bit) or 32-bit Windows is a requirement for your systems. If so, also please describe your setup. 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

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Incorrect secondary structure assignment in a .pdb
by Maciej Jagielnicki 30 Jun '18

30 Jun '18

Hi All, I used a combination of phenix real space refine and Coot to build a model into a cryoEM density map. I used an existing .pdb file as a starting point for my building. During the build, some helical elements became strands and vice versa (it was very clear to my eyes). Unfortunately, neither Phenix nor Coot would automatically update the header information for secondary structure elements, and I had to manually edit the header so that helices would show up in correct places when the .pdb file was viewed in Chimera or similar software. Not an ideal way of doing this which is likely related to what happened next. When the header information is removed, however, as it happens when the pdb.extract tool prepares a .pdb file for submission by turning it into a .cif file, the secondary structure elements are still displayed when a .cif file is visualized (bizzare in itself) but also the secondary structure is taken straight from the starting .pdb file (the one I used as a base for my model to which there is no connection whatsoever). The question is this - where does the incorrect secondary information come from in the absence of the header? How to fix this? I cannot deposit a file that shows helices/sheets wherever it wants... Regards, Maciej J. -- Maciej Jagielnicki, MS. Graduate Student University of Virginia Molecular Physiology and Biological Physics 480 Ray C Hunt Drive Rm 320 Charlottesville, VA Lab Phone: 434-243-2520

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Call for targets (not-yet-released structures) for CASP13 modelling experiment
by Randy Read 29 Jun '18

29 Jun '18

Posted on behalf of the CASP organizing committee: **** NB: There are only two weeks left to collect new targets for CASP13, so your contributions would be very gratefully received! **** Request for protein structures to test modeling methods - CASP13 CASP community experiments aim to establish and advance the state of the art in protein structure modeling. To this end, CASP collects information on soon-to-be released experimental structures for a three month season every two years. Sequences and other information on these targets is distributed to the protein modeling community, and the resulting models assessed by independent experts in the field. Results are published in special issues of the journal PROTEINS (see all about CASP12 at https://onlinelibrary.wiley.com/toc/10970134/86/S1). About 100 modeling groups from around the world take part. The success of CASP depends completely on the generosity of the experimental community in providing modeling targets. We are now requesting targets for the CASP13 experiment, which will launch at the beginning of May. So, if you have anything suitable, we would be most grateful if you would go to the target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, chemical crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if its available, it would be much appreciated!). For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and an experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. More details are available on the web site. Thanks, CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel, Switzerland ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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validating ~100 structures
by CPMAS Chen 27 Jun '18

27 Jun '18

Hi, All, I have about 100 structures needs be validated and optimized. what will be a fast way to do so? Can I somehow put phenix.molprobity in a circle? Thanks! -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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phenix.real_space_refine - Removing rotamer restraints on a per residue basis
by Ashley Pike 26 Jun '18

26 Jun '18

Hi, Is it possible to exclude particular residues from the effects of global restraints in phenix.real_space_refine? In my case rotamer restraints mucks up the sidechain fit to density for certain Phe and Tyr?. Thanks, Ashley

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Software Engineer position to work with Phaser team in Cambridge
by Randy Read 21 Jun '18

21 Jun '18

We've just advertised a position for a Software Engineer to work with us on the development of Phaser. Detailed information on the position and how to apply can be found on the University of Cambridge website (http://www.jobs.cam.ac.uk/job/17918/) and on jobs.ac.uk (http://www.jobs.ac.uk/job/BKS034/software-engineer). The text of the job description is appended, if you'd like to look at that before clicking on one of the links! Best wishes, Randy Read ================= We are looking for a graduate Software Engineer to join the group of Prof Read in the Cambridge Institute for Medical Research (http://www.cimr.cam.ac.uk/), based at the Cambridge Biomedical Campus in Cambridge. The well-established project develops mathematical methods and software for the imaging of biological molecules. The software supports academic and pharmaceutical R&D worldwide. You will be joining a small expert academic team. The successful applicant will have a careful approach to software development. Your software will be required to be reliable, algorithmically fast, and memory efficient. We have a slow development cycle and the code you write will be in use for the foreseeable future. Your individual contribution will be recognised with authorship of peer-reviewed articles; publications from our group have a track record of being highly cited. The project is funded by the National Institute of Health (USA) and the successful applicant will have the opportunity to join bi-annual collaborative meetings that cycle among Lawrence Berkeley National Laboratory (Berkeley, California), Duke University (Durham, North Carolina) and the New Mexico Consortium (Santa Fe, New Mexico). We also have an active collaboration with IBMB- CSIC (Barcelona, Spain). Software is open source (https://git.uis.cam.ac.uk/x/cimr-phaser/phaser.git/summary). We use the C++0x/C++11 standard to maintain cross-platform compilation and compatibility. You will have access to the University of Cambridge's computing resources, and a laptop will be provided. Qualifications and Experience: University degree that includes computer science and/or mathematics, experience with C++ and the Linux OS. Skills in Python scripting, GPU programming and threading would be desirable. Knowledge of biology to A level standard or equivalent would be an advantage. This appointment is full-time (37 hours/week Monday to Friday) but we welcome applications from individuals who wish to be considered for part-time working or other flexible working arrangements. Royalty payments from software will extend beyond the lifetime of the contract. University of Cambridge employment benefits include USS pension, and reduced staff fees for University of Cambridge graduate courses (see http://www.jobs.cam.ac.uk/offer/ for a full list). For more information on the research group see https://www.cimr.cam.ac.uk/research/principal-investigators/principal-inves…, and details of the Phaser project can be found at http://www.phaser.cimr.cam.ac.uk/. Fixed-term: The funds for this post are available untill 30th April 2022. ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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