- phenixbb - phenix-online.org

Problems about AutoSol: too many HA sites identified.
by Kaibo Zhang 10 Jul '18

10 Jul '18

Hello, I tried to use AutoSol to solve a SAD date set. The space group is P212121, with two proteins per ASU each containing one SeMet. However, the Hyss would always find 4~5 extra sites per ASU besides the two SeMet residues. So my questions are: a. Is this normal to have so many more sites identified? Or what might be the problem? b. Could I remove those extra Se sites during refinement if the occupancy is low or doesn't make sense biologically? Here are some details: 1. Most of the extra sites are around 20% occupancy and not within the range as alternate SeMet side-chain positions. One of them even overlapped with the position where should be a ligand phosphate. 2. The 2Fo-Fc map and AutoBuild solution looked fine, but the Fo-Fc map is kinda noisy with positive peaks showing up within the main-chain density which causes troubles for refinement. 3. No twining was detected for the dataset. Several space groups have been tried (including no screw axis) and all of the solutions contained more sites than there should be. Please let me know if you encountered similar problems before. Thanks a lot! Best regards Kaibo *Kaibo Zhang* PULSe, Purdue University Hockmeyer Hall, Room 321 240 S. Martin Jischke Drive, West Lafayette, IN 47907 Telephone: 765-337-1955 E-mail: zhang644(a)purdue.edu

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Detrmining pixel size
by anaa2 09 Jul '18

09 Jul '18

Hello, Does anyone know how to accurately determine the voxel size of an EM map? If you are slightly off (i.e. 1.38 compared to 1.40 pixel) does this affect real space refinement in PHENIX? Many thanks, Noor

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Real space refinement
by Reza Khayat 09 Jul '18

09 Jul '18

Hi, What is the syntax for having phenix.real_space_refine refine a single chain of a multi-chain complex? I have separated the chains into distinct files and run refinement on a single chain (file) with undesirable results. It seems that residues adjacent to the density of a neighboring chain get pulled into the neighboring density -possibly because the neighboring density is vacant. I hope my explanation is clear. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Fw: AsCA 2018/CRYSTAL 32 conference workshops
by Christopher Squire 07 Jul '18

07 Jul '18

? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Registration for the AsCA 2018/CRYSTAL 32 Conference workshops which will be held on Sunday, 2 December 2018 is now open. Delegates can register for a workshop at the same time as registering for the conference. There are four workshops which will each run concurrently. Spaces are strictly limited, so please register now at the following site: http://asca2018.org/registration/? Workshop topics: * Olex2-CCDC workshop * CCP4-Autorickshaw workshop * Combined workshop 1) SBGrid - Structural biology software infrastructure, 2) Synergistic use of diffraction and spectroscopic methods at XFEL and synchrotron sources * LCP - Lipidic cubic phase workshop For a full description of the workshops visit http://asca2018.org/workshops/ and for the full programme (including times) visit http://asca2018.org/programme/. Finally, a reminder that submissions are now open. Please visit the Call for Abstracts<http://asca2018.org/call-for-abstracts/> page for more information and to submit an abstract. Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, please do not hesitate to contact us using the email address below. Kind regards, Event Services University of Auckland Email: asca2018(a)auckland.ac.nz<mailto:[email protected]> [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

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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 07 Jul '18

07 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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