- phenixbb - phenix-online.org

running phenix.validation from command line
by Roberto Marabini 09 Apr '19

09 Apr '19

Hi, I see that it is possible to execute phenix.validation from command line by typing: phenix.validation_cryoem <path to>/5ni1.cif <path to>/molprobity.mrc resolution=2.2 The program runs smoothly and prints on screen a few hundreds of lines. The more or less equivalent program in version 1.13 was phenix.molprobity, when executed with the option pickle=True, phenix.molprobity saved to the hard-disk a pkl file containing all data. Is there an equivalent flag for phenix.validation_cryoem? where is the result of executing this shell being saved? thanks Roberto

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Clashscore and average B
by Sam Tang 08 Apr '19

08 Apr '19

Hello. I am refining a structure with Phenix.refine and encounter an issue which I appreciate your comments. The structure is in P1 and refined to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, Ramachandran favoured 97.5%. The statistics is acceptable to me but two numbers raised my concern. First is the clashscore of 7.7, which is below minimum of other structures shown by Polygon. Second is an average B of 37, with a minimum of 9.2. When I checked again in Coot (Average Temp fact. analysis), none of the residues or water look abnormal. I refined both individual and group B-factors and applied 'Optimize X-ray/adp weight'. So my questions are: (1) if a clashscore too high means a lot of bad contacts, how do you comprehend a clashscore too low? How can I modify my strategy to get around? (2) is there an acceptable low value of B? (I sort of went through a similar thread in phenixbb appeared 9 years ago but seems the discussion did not come to a conclusion). Any advice I should reliax or tighten the adp restraints? PS - it may be worth mentioning the structure contains a OMU nucleotide. The .cif file I used was generated by elbow. The nucleotide looks normal in coot w.r.t. contact or B-value. Thanks a lot! Sam

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X-Ray Methods in Structural Biology @CSHL
by Paul Adams 05 Apr '19

05 Apr '19

Dear All, The June 15th deadline for applications to the CSHL X-ray Methods in Structural Biology Course to be held later this year, October 15 through October 30, 2019 is rapidly approaching. The official course announcement is here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=19 so please pass this on to folks who might be interested and who would benefit. The course is designed for researchers who are either new to, or who wish to increase their in-depth knowledge of, macromolecular crystallography. This immersive course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers, which are combined with hands-on experiments. This 2019 course will be lead by Jim Pflugrath (Rigaku, ret.), Tassos Perrakis (NKI), Paul Adams (LBL), Janet Newman (CSIRO) and an All-Star cast of lecturers. Attendees can expect to participate in a course that is unparalleled in the world, with experts each devoting several days to teaching the fundamentals, theory and practical considerations of crystallographic structure solution. We expect to have the participants crystallize several proteins and determine their structures all in about two weeks.Students may also work on their own projects, but not exclusively. They will also become well-versed in the theory of X-diffraction and crystal structure determination while having lots of fun, but not much sleep. There will be a trip to the state-of-the-art beamlines at NSLS-II to collect data. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room and laboratory settings. Please check the above web link for more details. In particular, please note the information about fellowships, scholarships, and stipends that are available. It is often possible for applicants to receive some level of support to help offset the course fee. This course is supported with funds provided by the National Institute of General Medical Sciences for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. If anyone has any questions, please send me e-mail, I will be happy to answer any queries. Thanks for spreading the word, Janet, Tassos, Paul, and Jim -- 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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column labels for autobuild
by wtempel 04 Apr '19

04 Apr '19

Hi all,how does one specify column labels in a definition file for phenix.autobuild? input_files { map_file_is_density_modified = True input_map_labels = “F PHIDM FOMDM” input_refinement_labels = “F SIGF FreeR_flag” } gives this error: Sorry: Sorry, the label 'F SIGF FreeR_flag' does not exist (or all data is zero) … ...available labels are: ['FreeR_flag', 'F', 'SIGF', 'FC', 'PHIC', 'FC_ALL', 'PHIC_ALL', 'FWT', 'PHWT', 'DELFWT', 'PHDELWT', 'FOM', 'FC_ALL_LS', 'PHIC_ALL_LS', 'PHIDM', 'FOMDM', 'FDM', 'None'] Many thanks in advance. Wolfram Tempel

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Re: [phenixbb] Phenix elbow taxol
by r.joosten＠nki.nl 04 Apr '19

04 Apr '19

Before you make restraints yourself, check whether it is already in the dictionary. The name should be TA1 (http://ligand-expo.rcsb.org/reports/T/TA1/index.html). Cheers, Robbie On 31 Mar 2019 10:45, Georg Mlynek <georg.mlynek(a)univie.ac.at> wrote: Dear Ahmad, one way is to use the smiles string. If taxol if also named Paclitaxel then here it is: https://pubchem.ncbi.nlm.nih.gov/compound/paclitaxel#section=Canonical-SMIL… Then just watch this video on phenix.elbow https://www.youtube.com/watch?v=8qVYTUVKlbQ Br, Georg. On 31.03.19 08:08, Ahmad Khalifa wrote: How can I generate restraint files for taxol? I attached my taxol.pdb for reference. Thanks. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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Tantalum cluster
by Alexandra Deaconescu 02 Apr '19

02 Apr '19

Hello, I am trying to phase off Tantalum clusters. According to the Phenix documentation online, one should use TX as a scatter in Hyss. However, this does not work and Phenix complains about "unknown scatter type." Any ideas how to solve this? Thank you, Alexandra -- Alexandra Deaconescu, B.E., Ph.D. Assistant Professor Brown University Office: (401) 863-3215 Wet Lab: (401) 863-6729 Computational Lab: (401) 863-7031

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validation_cryoem
by Daniel Larsson 01 Apr '19

01 Apr '19

Hi, When I use the phenix.validation_cryoem command line tool, I get very little data compared to when I run the Cryo-EM validation from the GUI. Which options should I enable to get things like detailed clash annoation, CaBLAM analysis etc? 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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Phenix elbow taxol
by Ahmad Khalifa 31 Mar '19

31 Mar '19

How can I generate restraint files for taxol? I attached my taxol.pdb for reference. Thanks.

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Call reminder: XChem fragment screening, NEXT WEDNESDAY
by Frank von Delft 29 Mar '19

29 Mar '19

Dear aspiring drug discoverers A reminder that the deadline for the next round of proposals for XChem fragment screening is *next Wednesday 5pm*, as part of Diamond's general Call for Proposals. Full details <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Applying-for-XC…> are on the XChem webpage <https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html>. *Reminder: *we are now inviting a broader set of projects: * Two-tiered access: if you have an exciting system but don't yet know how to progress it, you can ask for exploratory access ("Tier 1") * BAG access: several labs and collaborations have requested increased flexibility, and several have been assigned Block Allocation Groups. If you wish to submit this route, I suggest you also email me directly. Happy screening! Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile)

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scattering_table in phenix.real_space_refine
by Keitaro Yamashita 25 Mar '19

25 Mar '19

Dear PHENIX developers, For the refinement of CryoEM structure, I changed scattering_table to electron from default (n_gaussian in phenix-1.13), but the resultant coordinates and ADPs were exactly same while map-model CCs were improved. Looking into the code, I noticed scattering_table is not passed to the ADP refinement code (mmtbx.refinement.real_space.adp.real_space_group_adp_refinery_via_reciprocal_space) and xray_structure is newly constructed from a pdb_hierarchy object; therefore a default table in scattering_type_registry() (which is n_gaussian) is always used. Is this an intended behavior? I modified the code to use the scattering table of electron in ADP refinement, and CCs were improved (CC_mask 0.7566 to 0.7813; both evaluated with scattering_table=electron). Best regards, Keitaro

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