- phenixbb - phenix-online.org

stuck with phenix refine
by intekhab alam 30 Aug '10

30 Aug '10

Hi I am working with a twinned data set having R32 space group. when i tried to refine with phenix refine using the twin option it got stuck after some time. There is no error message showing up and the refinemnet donot progresses further. I have used the twin law suggested by Xtriage program in Phenix. Kindly help me out. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Re: [phenixbb] phenix.automr questions
by Kay Diederichs 29 Aug '10

29 Aug '10

Dear Randy, Nat, Tom, thank you for pointing out the existence of phenix.phaser to me, and sketching its usage. I think I'll make my way with that information; nevertheless it would be great if it were officially documented (Google returned nothing to me about phenix.phaser). BTW, I'm trying to put together some orthogonal Phenix documentation at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix . I take the opportunity to state that although the URL refers to the CCP4 users' wiki, and obviously Phenix is not part of CCP4, the wiki covers a broad range of crystallographic information. Thus, I do think it is appropriate to collect Phenix-related information (from a user perspective) there, and would like to invite everybody to contribute to the Phenix entry (and others!). thanks, Kay

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Re: [phenixbb] phenix.automr questions
by Kay Diederichs 29 Aug '10

29 Aug '10

Hi Tom, thanks for answering my questions! Yes, it would be good to have a flag to turn off the inverse hand because a) having the possibility to look at each spacegroup offers a very effective way of parallelization b) if I "grep" the spacegroup name in the logfile I find: dikay@turn10:-2010/phenix.automr% grep "P 4" mf92.log Space group: P 41 21 2 (No. 92) LIST OF ALL PLAUSIBLE SG: ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2'] Space group: P 41 21 2 (No. 92) NEW dictDATA {'raw_data': [' P 4abw 2nw', (101.71700286865234, 101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0), <scitbx_array_family_flex_ext.double object at 0xe554a10>, <scitbx_array_family_flex_ext.double object at 0xe554bd0>, <cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]} space_group : P 41 21 2 all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2'] dictDATA: {'raw_data': [' P 4abw 2nw', (101.71700286865234, 101.71700286865234, 344.74798583984375, 90.0, 90.0, 90.0), <scitbx_array_family_flex_ext.double object at 0xe554a10>, <scitbx_array_family_flex_ext.double object at 0xe554bd0>, <cctbx_array_family_flex_ext.miller_index object at 0xe4716c0>]} HALL: P 4abw 2nw P 43 21 2 P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) Space-Group Name: P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) P 43 21 2 * P 41 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 P 43 21 2 P 41 21 2 * Space-Group Name (Number): P 41 21 2 (92) Fast Translation Function Table: Space Group P 41 21 2 Best Space Group so far: P 43 21 2 Space Group Name (Number): P 41 21 2 (92) Packing Table: Space Group P 41 21 2 Space-Group Name (Number): P 41 21 2 (92) Refinement Table (Unsorted): Space Group P 41 21 2 Refinement Table (Sorted): Space Group P 41 21 2 Space-Group Name (Number): P 43 21 2 (96) Best spacegroup from search with first component in permutation: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Best spacegroup from search with first component in permutation: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Fast Translation Function Table: Space Group P 43 21 2 Space Group Name (Number): P 43 21 2 (96) Packing Table: Space Group P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) Refinement Table (Unsorted): Space Group P 43 21 2 Refinement Table (Sorted): Space Group P 43 21 2 Best Space Group: P 43 21 2 Space-Group Name (Number): P 43 21 2 (96) which shows that at a certain point the MTZ file's spacegroup is abandoned and the calculation finishes in the enantiomorph spacegroup, which has the drawback that I cannot really compare the best (complete) results of both enantiomorphs. And with one good and three bad search models I don't know if abandoning the given spacegroup early is definitively the right decision (but it's hard for me to tell exactly what criterion the decision was based upon - it may have been after an exhaustive search in #92 in which case my worry would not be justified). thanks, Kay > Message: 2 > Date: Sat, 28 Aug 2010 09:07:08 -0600 (MDT) > From: "Thomas C. Terwilliger"<terwilliger(a)lanl.gov> > To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.automr questions > Message-ID:<14563.128.165.0.81.1283008028.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Kay, > > I'll answer what I can; perhaps Randy the others may have more comments. > >>> Dear developers, >>> >>> I have four questions concerning phenix.automr (I'm using version 1.6.4): >>> >>> a) is there a way to make the program try all permutations for the >>> search order of my four search molecules, or do I have to write a script ? > > It would be a good idea for me to put that in. For now, yes, you have to > make a script to do that. > >>> >>> b) how can I completely switch off the search in the alternative >>> spacegroups - I am under the impression that although the "effective >>> parameters" are >>> all_plausible_sg_list = None >>> use_all_plausible_sg = False >>> the search is not only done in the spacegroup I specified (#92=P41212) >>> but also in #96=P43212 . I believe so because the output says: >>> ... >>> 2 alternative spacegroups >>> SpaceGroup will be determined by highest LLG in search for FIRST >>> ensemble >>> Search order: >>> P 43 21 2 >>> P 41 21 2 >>> ... >>> (I would rather run a second search "manually" in the other spacegroup!) > > Yes, it runs the inverse hand even if you say > "use_all_plausible_sg=False". However it should not run all the other > space groups (all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', > 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2']). I'll see > if we can put in a flag so it doesn't run the inverse hand if you don't > want it to. > > >>> >>> c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the >>> latter is symlinked to the former). Am I right that I could just leave >>> out one of them? I did this after looking at >>> http://www.phenix-online.org/documentation/automr.htm#anch70 but I >>> wonder which of the specifications of sequences and masses overrides the >>> other one? or is the first specification used for editing the search >>> models, and the second for getting the likelihood terms right? > > Looking at your parameters file, I see what you mean. If you supply two > different files, then yes, the one you specified at the top of your file > with "seq_file=all.dat" is going to be used for editing the file for > autobuild, and the one you specified in the scope "component" is going to > be used for getting the likelihood terms right. > > Normally (always?) these should be the same. So normally, just supply the > first one "input_seq_file=seq.dat") and it will be used for both purposes. > > Or if you have several components, only specify them in the "component" > scopes, and all of them will be put together into a single file and used > as the input to autobuild. > > >>> >>> d) what kind of editing is done? Is phenix.sculptor run internally? I >>> find {a,b,c,d}_edited.pdb but are they actually used? > > Only basic editing to make the model compatible with autobuild is done. No > sculpting is done inside automr for now. > > All the best, > Tom T

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phenix.automr questions
by Kay Diederichs 29 Aug '10

29 Aug '10

Dear developers, I have four questions concerning phenix.automr (I'm using version 1.6.4): a) is there a way to make the program try all permutations for the search order of my four search molecules, or do I have to write a script ? b) how can I completely switch off the search in the alternative spacegroups - I am under the impression that although the "effective parameters" are all_plausible_sg_list = None use_all_plausible_sg = False the search is not only done in the spacegroup I specified (#92=P41212) but also in #96=P43212 . I believe so because the output says: ... 2 alternative spacegroups SpaceGroup will be determined by highest LLG in search for FIRST ensemble Search order: P 43 21 2 P 41 21 2 ... (I would rather run a second search "manually" in the other spacegroup!) c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the latter is symlinked to the former). Am I right that I could just leave out one of them? I did this after looking at http://www.phenix-online.org/documentation/automr.htm#anch70 but I wonder which of the specifications of sequences and masses overrides the other one? or is the first specification used for editing the search models, and the second for getting the likelihood terms right? d) what kind of editing is done? Is phenix.sculptor run internally? I find {a,b,c,d}_edited.pdb but are they actually used? thank you, Kay P.S. I run with "phenix.automr mr.eff" where mr.eff is automr { data = "m879_2_rg92.mtz" seq_file = all.dat ensemble { ensembleID = "mol1" copies_to_find = 1 coords = a.pdb identity = 80 } ensemble { ensembleID = "mol2" copies_to_find = 1 coords = b.pdb identity = 45 } ensemble { ensembleID = "mol3" copies_to_find = 1 coords = c.pdb identity = 45 } ensemble { ensembleID = "mol4" copies_to_find = 1 coords = d.pdb identity = 45 } component { component_type = *protein nucleic_acid seq_file = all.seq component_copies = 1 } autobuild_variables{ n_cycle_rebuild_max = 1 } }

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Phenix error running MIR-example
by Shankar Prasad Kanaujia 29 Aug '10

29 Aug '10

Dear Developers/Users, I am getting an error while running "rh-dehalogenase-mir" example provided in the phenix example. I am using phenix 1.6.4 version. It runs properly using the command "phenix.run_example rh-dehalogenase-mir", whereas, it gives error in GUI mode. I am attaching the picture of my input and error (in the right-top corner). Please let me know the reason of this error. -- Yours Sincerely, Shankar Prasad Kanaujia Research Student C/O - Dr. K. Sekar Bioinformatics Centre, SERC Indian Institute of Science, Bangalore-12 Phone - 9480258032 Office - 080-2293-3059

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Postdoctoral position in Protein X-ray Crystallography
by cdas＠purdue.edu 29 Aug '10

29 Aug '10

Applications are invited for a postdoctoral research position in the Das Lab, Department of Chemistry, Purdue University, West Lafayette, IN, USA. The position requires the applicant to work on structural and biochemical characterization of ubiquitin hydrolases (deubiquitinases) and their complexes with substrates, cofactors and inhibitors (see Boudreaux et al, PNAS, 107, 9117 (2010)). The applicant is also expected to work on an ongoing collaborative project on method development related to imaging of protein crystals (of ubiquitin hydrolases and others) using second order non-linear optical methods. We are looking for highly motivated candidates with extensive experience in biochemical studies, crystallization and structure determination of proteins by x-ray crystallography. Specifically, the candidate is required to have hands-on experience with protein purification, crystallization, X-ray data collection, structure determination and structural analysis. Applicants should send their CV and the names and contact information of at least three references via email to: Chitta Das Assistant Professor Department of Chemistry Purdue University 560 Oval Drive West Lafayette IN, 47907 Email address: cdas(a)purdue.edu

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Can Phenix refine B factors for several residues only?
by zhangh1＠umbc.edu 29 Aug '10

29 Aug '10

Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Is there anyway Phenix can do this? Thanks for any suggestions! Best Regards, Hailiang

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Re: [phenixbb] advice for refinement with anomalous information
by John Rose 27 Aug '10

27 Aug '10

Hi, I am refining my first structure (Cd-SAD) with the Phenix (GUI) and would like to refine anomalous f' and f". When i check the box, a menu appears and I have no idea of how to define the Cd atoms. I looked at the help and FAQ and found this: refinement.refine.anomalous_scatterers { group { selection = name BR f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime So I thought the name should be input as CD in the gui but when I submitted the refinement I got an error. Any help here would be appreciated? Thanks, John Rose

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file type not supported???
by Joseph Noel 24 Aug '10

24 Aug '10

Hi All, I am having a problem that should be totally simple but I am stuck trying to find out what is happening. I use Text Wrangler on my Mac as a text editor of files. I have used it many many times to edit PDB files. It seems now that some PDB files that I have opened and removed a few lines now show up as an unrecognized file type when trying to read them into Phenix or into COOT. However, when I upload them on the Molprobity site they are read fine and processed. However, even the downloaded file from Molprobity gives the same error. I know it must be something simple but stumped and hoping someone else has experienced the same problem and has a quick fix. Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] phenix.ready_set hydrogens not compatable with coot library
by Joseph Noel 24 Aug '10

24 Aug '10

Hi All, Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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