- phenixbb - phenix-online.org

How to use phaser gyre and gimble in phenix
by Meinke, Gretchen 18 Jul '18

18 Jul '18

Hi! I have a challenging MR problem and maybe phenix.phaser gyre and gimble will help. My molecule is flexible horsehoe shaped slinky, there are multiples in the unit cell (maybe 8-12??). My data is medium resolution 3.5 maybe. There are good homology models (also flexible!) It seems to have 1-2 hinge points (or 2-3 domains). I saw your publication "Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement" Acta Cryst. (2018). D74, 279–289 and that describes exactly what I would like to do. One problem, I cannot at all figure out how to use gyre in gimble in phenix. I cannot find it in the GUI, and am unclear how to run it as a script. It looks super useful and would love to use it. Any help, a script, etc would be most appreciated! Thanks! Gretchen

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FW: Occupancy / alternate conformation Refinement
by Schulz, Eike-Christian 17 Jul '18

17 Jul '18

Dear all, In one of my structures I appear to have a mixed state between a covalently bound intermediate and the free substrate occupying _almost_ the same position. I can model the states nicely in coot, but during refinement the molecules “fly” apart - although the occupancy was limited to 0.5 for their overlapping atoms. I have tried to model the free ligand as an alternate conformation of the covalent intermediate: HETATM 852 N ASB A 110 10.523 15.702 10.022 1.00 14.48 N HETATM 853 CA ASB A 110 9.974 15.713 8.664 1.00 15.11 C HETATM 854 C ASB A 110 8.635 16.385 8.683 1.00 14.31 C HETATM 855 O ASB A 110 8.563 17.443 9.233 1.00 13.03 O HETATM 856 CB ASB A 110 10.053 14.307 8.091 1.00 11.72 C HETATM 857 CG ASB A 110 9.774 14.157 6.621 1.00 15.26 C HETATM 858 OD1 ASB A 110 10.688 14.485 5.644 1.00 19.29 O HETATM 859 OD2 ASB A 110 8.693 13.880 6.340 1.00 13.36 O HETATM 860 C1 AASB A 110 10.637 15.649 3.353 0.50 27.61 C HETATM 861 C2 AASB A 110 10.231 14.480 4.266 0.50 32.98 C HETATM 862 O1 AASB A 110 11.505 16.454 3.690 0.50 31.63 O HETATM 863 O2 AASB A 110 10.085 15.787 2.280 0.50 21.80 O HETATM 4742 O2 BASB A 110 10.072 15.815 2.191 0.50 24.78 O HETATM 4743 C1 BASB A 110 10.573 15.717 3.221 0.50 28.20 C HETATM 4744 O1 BASB A 110 11.449 16.458 3.619 0.50 22.71 O HETATM 4745 C2 BASB A 110 10.107 14.567 4.152 0.50 19.02 C HETATM 4746 F BASB A 110 9.287 13.735 3.610 0.50 34.13 F Although I have provided a new CIF file for the ligand named according to the alternate conformation this causes phenix to crash. How can I correctly refine these overlapping atoms ? Thanks for your advice, Eike

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n_gaussian tables?
by Aaron Oakley 16 Jul '18

16 Jul '18

Hi Phenixers, I gather that the wk1995 and it1992 scattering tables come from Waasmaier & Kirfe (1995), Acta Cryst. A51, 416-431 and the International Tables Vol C 1992 respectively. Can someone please tell me from where the n_gaussian scattering tables are derived? With thanks, a++

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Problems about AutoSol: too many HA sites identified.
by Kaibo Zhang 09 Jul '18

09 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 08 Jul '18

08 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 08 Jul '18

08 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 06 Jul '18

06 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 06 Jul '18

06 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 06 Jul '18

06 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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