May 2015 - phenixbb - phenix-online.org

Re: [phenixbb] Refinement
by Pavel Afonine 26 May '15

26 May '15

Hi Mohamed, > How do tell phenix.refine to not move my HEM ligand around? yes, you can exclude selected atoms from refinement of coordinates in Phenix refinement GUI: Refinement settings -> Modify selection for: XYZ coordinates -> Edit -> type atom selection in "Edit selected" field (under XYZ refinement) like "chain A and resseq 1" or "chain A and resname ATP" However, I would rather find why correct geometry is not preserved. > I have a cif file describing the ligand but in my case, I can see > clear density of it not following the ideal geometry. If you send me files (off mailing list of course!) I will see if I can explain it.. You can copy to Nigel too as chances are that if you choose to send files I will be talking to him anyway. > As an example, I have attached a screenshot from Coot. It's hard to infer what's going on from a static image.. > In fact, the C atom is covalently linked to the nearest Cys, so the > HEM side chain should be 'moved' into the density and the green blob > shouldn't be there. Is this link defined anywhere in restraints used in refinement? Pavel

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Fw: on the convergence of phenix refine
by Smith Liu 26 May '15

26 May '15

Dear All, For the meaning of non-convergence here, I mean in the whole 30 macro-cycles, both the Rwork and Rfree curves were in zigzag format, which I never met before. I am looking forward to getting an explanation from you. Smith -------- Forwarding messages -------- From: "Smith Liu" <smith_liu123(a)163.com> Date: 2015-05-26 09:26:23 To: phenixbb(a)phenix-online.org Subject: [phenixbb] on the convergence of phenix refine Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

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on the convergence of phenix refine
by Smith Liu 26 May '15

26 May '15

Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

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on B-factor refine of the phenix.real_space_refine
by Smith Liu 23 May '15

23 May '15

Dear Pavel, For the input, the last line of PDB is as followng, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00100.56 H For the run=ADP of the phenix.real_space_refine, the last line of the first model of all states pdb is, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00194.44 H and the last line of the second model of all states pdb is ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00164.47 H. Clearly in each PDB of each model of the all states pdb produced, the b-factor is different, and they are different with the b-factors of the input pdb. Thus will you please explain why there are 2 states pdbs which seems both are refined pdbs? In addition, is it normal that the single state refined pdb cannot be opended? Next, will you please explain based on what of the mrc file, the phenix.real_space_refine run=ADP function got the b-factors? Further, I have noticed that the phenix.real_space_refine run=ADP gave a resolution which is different from the mrc general resolution given by relion or some other software. Will you please explain base on what the phenix.real_space_refine run=adp gives the resolution? Best regards. Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-23 00:48:00 To: "Smith Liu" <smith_liu123(a)163.com>,"phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: Fw:Re: [phenixbb] on B-factor refine of the phenix.real_space_refine For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB Yes I think so.. Is it not? Pavel

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Fw:Re: on B-factor refine of the phenix.real_space_refine
by Smith Liu 22 May '15

22 May '15

Dear Pavel, It looks work. But for the refined PDB, it seems it was in read-only format, which I cannot copy. For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB, am I right? Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-21 14:44:30 To: "Smith Liu" <smith_liu123(a)163.com>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] on B-factor refine of the phenix.real_space_refine I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， no need to convert .mrc into .ccp4 (isn't it the same thing?). Anyways, phenix.real_space_refine can use both. and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. I need to see the files to be able to comment. If you share the files (off list and not sending directly via email but using things like Dropbox instead) then I will be happy to have a look. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? phenix.real_space_refine model.pdb map.mtz run=adp should just do what you want. If it didn't - see above (I need to see the files). Pavel

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metal-ligand distances, and Optimize X-ray/stereochemistry weights
by Emilia C. Arturo (Emily) 21 May '15

21 May '15

I'm refining a model at 2.9 A, where four chains are in the ASU, and each active site has an iron with a few ligands; the configuration of this active site is the topic here. Currently the iron-ligand distances are not ideal (according to CheckMyMetal and the ideal distances generated by phenix.metal_coordination), but they are within a range observed previously for structures of truncated versions of this enzyme; furthermore, the more the metal-ligand distances change towards ideal distances, the more positive and negative density I observe in the Fo-Fc, so it appears that this deviation from the 'ideal' is supported by the data. However, when I use the 'Optimize X-ray/stereochemistry weights' option during refinement, the metal-ligand distances change (the metal appears to do most of the moving), getting closer to ideal, and this generates more positive and negative density in the Fo-Fc map). However, clearly it's nice that optimizing the X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work ratio fine as well). So what is the most appropriate approach here, in order to keep the metal-ligand distances that best support the data, but still reap the benefits of the optimized stereochemistry weights? Some details of the structure and refinement are these: The iron in each of the four chains in the ASU is coordinated with atoms from two histidines, a glutamate, and a water (so four ligands per Fe) and there remains un-modeled density in the iterative build comp OMIT map used for modeling (because resolution is 2.9A and adding more water (which is my best guess, given what truncated structures at higher resolution show coordinating the Fe) does nothing to the Rf). I am working with an .edits file generated by phenix.metal_coordination. After some experimentation, I've left the sigma values (for Fe-O and Fe-N) at default values, and added a restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma value of 0.1. Emily.

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Your abstract can still be considered for an oral presentation at the American Crystallographic Assn Annual meeting
by Terwilliger, Thomas Charles 21 May '15

21 May '15

Hi Phenix users, A message from the American Crystallographic Association! YES! We are still accepting abstracts. No late fee. ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. see: http://www.AmerCrystalAssn.org All the best, Tom T Vice-President, ACA

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on B-factor refine of the phenix.real_space_refine
by Smith Liu 21 May '15

21 May '15

Dear All, I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? Smith

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Map quality
by mohamed noor 19 May '15

19 May '15

Dear all Is there a single (or a few) metrics that can be used to quantitatively assess map quality instead of looking at each one in Coot? For example, I want to compare the effect of having low completeness in the low resolution shells. Thanks.

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Several postdoc opportunities, Shanghai University
by Pavel Afonine 18 May '15

18 May '15

Posted on behalf of Prof. Ren Wei and Jeffrey Reimers. **************************** *Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray Crystallographic Structures and related work in Biophysics, Biochemistry, Biomaterials, Chemistry, and Soft Condensed Matter*** Shanghai University (http://www.shu.edu.cn) isseeking multiple outstanding postdoctoral researchers to be part of the newly created International Centre for Quantum and Molecular Structure (ICQMS). Parallel Adjoint Appointments at The University of Technology, Sydney (UTS) (http://www.uts.edu.au/about/faculty-science/physics-and-advanced-materials), Department of Mathematical and Physical Sciences, will also be available. Most available positions relate to the core project of ICQMS: the development of codes for automatic quantum refinement of protein crystallographic structures. For these positions, previous experience at the PhD or post-doctoral level in the simulation of protein structure is essential. This could involve mastering of quantum-chemical software, molecular dynamics methods, statistical mechanics theories, or protein structure refinement. Positions are available for both software users and methods developers. ICQMS also has a wider view, considering the determination of protein function and spectroscopy, especially for photosynthetic proteins, understanding the effects of solvation and environment on molecular properties, quantum dynamics and coherence in proteins, understanding order/disorder transitions, the fundamental role played by entropy in controlling protein structure, the properties of biomaterials such as cement, general self-assembly processes such as organic self-assembled monolayer formation and properties, and the properties of bulk materials. A position is also available concerning the development and application for GPUs of Hartree-Fock theory or Density-Functional Theory or molecular dynamics. All positions require a PhD in Chemical Physics, Quantum Chemistry, Computational Biochemistry, Crystallography, or related disciplines. Excellent verbal and written communication skills in English are essential. Proven independence is also essential. Candidates that have contributed to scientific-community activities and/or teaching innovation will be considered favourably, as will those that have contributed independently to multidisciplinary team projects. Shanghai University is a well funded, internationally connected, rapidly raising University with a strong profile in Material Science, and indeed under the direction of University President Prof. H. J. Luo is a central player in the extensive Chinese Materials Genome Initiative (MGI) Project. ICQMS extends this vision into mainstream chemical and biochemical research. Adjunct Appointments at the University of Technology Sydney will allow each Postdoctoral Fellow to spend 6 months doing joint research in Sydney with UTS staff. Shanghai University and The University of Technology Sydney have a 20-year history of close collaboration, including the joint Smart Cities Institute and the Sydney Institute of Language and Commerce. This collaboration also includes the dual PhD degree program between the two universities. The negotiable anticipated start date is 2015 between August and December. The positions are available for two years and renewable subject to a performance review. Shanghai University is an Equal Opportunity Employer and all persons are encouraged to apply. Applicants should send their curriculum vitae including lists of publications, summaries of their research interests, lists of prizes and awards, summaries of any teaching, community service or administrative experience, and have three reference letters sent directly to yarulove2006(a)shu.edu.cn <mailto:[email protected]>. Further information can be obtained from: ICQMS Director: Jeffrey Reimers reimers(a)shu.edu.cn <mailto:[email protected]> or ICQMS Deputy Director: Wei REN renwei(a)shu.edu.cn <mailto:[email protected]> Closing Date: 2015 December 31^st , or until all positions are filled.

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