- phenixbb - phenix-online.org

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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Refinement
by StrBio 23 Mar '19

23 Mar '19

ALL. I have data at 2.4 A in P21 sp gr, helical protein. Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics oither Rfactor (by Phenix). Refmac quit same. Should I deposit it or look better data? Any suggestion?

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Phenix Rosetta hybrid refinement PHENIX_ROSETTA_PATH error
by Ahmad Khalifa 23 Mar '19

23 Mar '19

But I have the path set! (base) [labusr@luxor ~]$ echo $PHENIX_ROSETTA_PATH /home/labusr/rosetta:/home/labusr/rosetta/main I attached the log. Please advise.

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Distance constraint to atom in symmetry copy in phenix.refine
by Julian Esselborn 22 Mar '19

22 Mar '19

Dear community, we have a somewhat complicated problem to which I don't seem to find a solution. We have a structure, which has a number of 3-fold and 2-fold symmetry axes in the final assembly structure. The 3-fold axes are hold together by metal atoms on the axis. However, we have three cases of these axes: 1. Symmetry axis falls onto the crystallographic symmetry axis. We can deal with this; setting metal to 0.33 occupancy and setting metal-protein distance constraints. This is a proper symmetry axis. 2. Symmetry axis doesn't fall onto a crystallographic symmetry axis, but all three monomers coming together are within the same symmetry copy of the ASU. Even easier, metal stays at occ=1 and we just set constraints to chain A, chain B, chain C. 3. The really challenging case, where the axis doesn't fall onto the symmetry axis, but the three monomers coming together are in different symmetry copies of the ASU. Cases (2) and (3) are pseudo-symmetric in the crystallographic sense. Usually a bit of intelligent moving around of the monomers to their crystallographic symmetry positions should push all monomers of case (3) into neighboring positions within the same ASU ending up as case (2); problem solved. BUT: In our structure we have too many 3fold axes, such that there will always be one of them ending up as case (3). E.g. the three monomers are chains A, B, C, but they do not end up neighboring in the ASU. Rather the axis is formed by A, B' and C'' (with ' denoting different symmetry copies of the ASU). We could assign the metal to chain A with occ=1 and no metal in B and C. However, we would need to set a distance constraint from the metal to it's ligands in protein monomer B and protein monomer C. But it is only the ligand in B' and C'', which are actually close to the metal in A. The ligands in B and C are at the other end of the ASU. Is there a way to set a distance constraint such that it measures the distance to a crystallographic symmetry copy? A different idea was to just assign an alternative position alt A, alt B and alt C to the metal, with A being close to the ligand in monomer A, B close to monomer B and C close to monomer C. That way we could make constraints. But we would need to cross fingers that the three metal atoms actually end up in the same spot once applying the crystallographic symmetry (and remember, that 3-fold axis is not constructed by applying a 3fold rotational symmetry around that axis; rather an actual crystallographic symmetry somwhere else brings them together; means the ligands with their metal atoms can actually move independently). I'm a bit at a loss how to deal with this and would appreciate input. Thanks a lot in advance! all the best Julian ---- Julian Esselborn Postdoctoral Researcher Tezcan group University of California, San Diego

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Map Segmantation
by Yangqi Gu 21 Mar '19

21 Mar '19

Hi Everyone, I have a naive question about segmentation. I have a low resolution map of a filament (~20 A) and I know the helical symmetry. I have monomer sequence but no structure. I am wondering if I could segment the filament and obtain the monomer density? Does segment_and_split_map work on the low resolution case? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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