March 2019 - phenixbb - phenix-online.org

HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop - HANDS 2019
by Meilleur, Flora 22 Apr '19

22 Apr '19

First announcement HANDS 2019 HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop Oak Ridge, TN. June 19 - June 14, 2018 Oak Ridge National Laboratory, in conjunction with North Carolina State University, and support from the National Science Foundation and the Shull Wollan Center - a Joint Institute for Neutron Scattering, celebrates a decade of neutron scattering education in structural biology at ORNL with the HFIR/SNS Advanced Neutron Diffraction and Scattering workshop (HANDS 2019). Detailed information can be found on the workshop web page: https://conference.sns.gov/hands2019/ Application deadline: April 29, 2019 Fellowships to support travel and accommodation are available. No registration fee. The workshop aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Participants of HANDS 2019 will become familiar with neutron techniques with hands-on experiments in sample preparation, crystallography, small angle scattering, reflectometry and neutron spin echo. The workshop is designed for graduate students, post-doctoral fellows and faculty with limited to no experience with neutron sciences. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Scattering Division Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

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12th CCP4/APS Crystallographic School in the US
by Xu, Qingping 11 Apr '19

11 Apr '19

Dear Colleagues, We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php. Dates: June 17 through 24, 2019 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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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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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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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 24 Mar '19

24 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 23 Mar '19

23 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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