- phenixbb - phenix-online.org

question on bad geometry
by fn1＠rice.edu 01 Sep '10

01 Sep '10

Hi everyone, I have a structure at 2.3 A refined in phenix to R/Rfree=0.23/0.28. However, the geometry is not that good, the followings are the output from phenix.model_vs_data, Stereochemistry statistics (mean, max, count): bonds : 0.0080 0.0547 3244 angles : 1.1669 12.1085 4374 dihedrals : 15.7241 85.6280 1202 chirality : 0.0706 0.2831 536 planarity : 0.0036 0.0246 573 non-bonded (min) : 2.1217 Ramachandran plot, number of: outliers : 17 (4.02 %) allowed : 37 (8.75 %) favored : 369 (87.23 %) Rotamer outliers : 30 (8.62 %) goal: < 1% Cbeta deviations >0.25A : 0 All-atom clashscore : 40.51 (steric overlaps >0.4A per 1000 atoms) I tried to use fix_rotamer=True, but it doesn't help at all. As to the rotamer outliers, the value is far higher than the ideal one. Does that mean I need to manually adjust the model? Or will autobuild help improve the geometry? Thanks! Fengyun

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How to do a phenix.fmodel calculation incorporating the exponential scaling model only?
by zhangh1＠umbc.edu 31 Aug '10

31 Aug '10

Hi, I want to use phenix.fmodel to do a calculation incorporating the exponential scaling model only (Not the flat model). I am not sure whether I just need simply specify: mask { use_asu_masks = False } since the output maps are just identical no matter use_asu_masks = True or False. Should I do something else to enable exponential scaling model only? Thanks! Best Regards, Hailiang

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0.00 Refined Isotropic ADPs
by Joseph Noel 31 Aug '10

31 Aug '10

Hi All. Me again! LOL I am sure this has come up and related to how the "B-factor" in the refined PDB's ADP column is calculated including the overall anisotropic B-factor, etc but is it unusual to have isotropic ADPs refine to 0.00? I have several nice structures with 0.00 isotropic ADPs. I am not refining TLS or anisotropic ADPs at all. Just the normal course of refinement. These are regions of a high degree of order and the maps are beautiful but just wandering what the 0.00 ultimately means particularly when I eventually submit to the Protein Data Bank. Joe P.S. Nat's tips on COOT and Phenix are working beautifully now! Thanks Nat! ___________________________________________________________ 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 and COOT Together on a Mac (and Probe too?)
by Joseph Noel 31 Aug '10

31 Aug '10

Nat, One thing that seemed to solve all the problems at once was to completely remove any reference to the COOT path in the Phenix preferences! Is that weird? When I removed it completely only leaving the path to PYMOL then COOT is working just fine in conjunction with Phenix and even the Probe issues have disappeared. Prior to this, I was tried two different paths to COOT. 1. /sw64/bin/coot 2. /Applications/coot.app/Contents/MacOS/coot Neither behaved but if I don't specify anything it works. 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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Problem with low figure of merit
by sankaranarayanan srinivasan 31 Aug '10

31 Aug '10

Hi all, I am new to structure solving. I have a 2.9A dataset for a Seleno crystal of which i am trying to use Autosol to build an initial map. I used the settings for a thorough solution, instead of quick. All the other parameters were set to default settings. The solution that i got from autosol, gave me the following result Solution # 1 BAYES-CC: 23.7 +/- 30.9 Dataset #1 FOM: 0.27 Residues built: 238 Side-chains built: 139 Chains: 15 Overall model-map correlation: 0.65 R/R-free: 0.38/0.42. Score type: SKEW CORR_RMS Raw scores: 0.02 0.77 100x EST OF CC: 16.86 32.11 The density modification map matches, quite well with many of my side chains fitted. My question here is , IS THERE A WAY I CAN IMPROVE THE Figure Of Merit , BY CHANGING ANY PARAMETERS IN PHENIX-AUTOSOL. I HAVE A HIGH SOLVENT CONTENT IN MY CRYSTAL AND I DID NOT INPUT THAT IN MY INITIAL PARAMETERS. DOES PHENIX AUTOSOL CONSIDER SOLVENT FLATTENING FOR SUCH CRYSTALS? I would appreciate someone's help in this regard Thanks Shankar

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Phenix and COOT Together on a Mac (and Probe too?)
by Joseph Noel 30 Aug '10

30 Aug '10

Hi All, I am having trouble getting COOT to link up with Phenix. I know that Bill Scott's fink version of COOT breaks the link but I have also tried the stand alone latest version for Mac OSX without success. I suspect there may be something additional I need to set up to get the two programs to talk to one and other. I can open COOT with the GUI link in Phenix but that's it. The two do not communicate and the "Phenix button" does not appear. I am running everything on a Mac laptop with an Intel chip and the latest snow leopard operating system. I can also run probe independently in COOT using the script suggestion for the .coot file from the MOLPROBITY web site. However, after several checks of bad contacts the system freezes at the level of XQuartz and I have to kill X-Windows to start over. I don't know if this is in someway linked to the problem getting COOT and Phenix to talk to one and other but I thought I would throw it out there. Finally, if I do run COOT by starting it from the Phenix GUI it also freezes after several rounds of building, etc just like the probes to check for clashes. If anyone has observed this behavior and has some suggestions I would much appreciate it! Its not a big deal as I can run things separately and work from a print out of Molprobity outliers but it would be sure nice to just click and correct. Sorry to keep going but I should say I have Bill Scott's fink'ed version of coot installed in as directed in /sw64 and the stand alone version installed along with CCP4 and Phenix in my Mac's /Applications directory where all my standard Mac apps appear. 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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Can we untoggle molecular weight mean deviation check on ensembles in autoMR?
by James R. Thompson 30 Aug '10

30 Aug '10

Can folks untoggle the molecular weight mean deviation check in phenix.autoMR on the ensembles input? I want to use an ensemble of coordinates generated by the Mustangs server from a SSM alignment. Therefore, by design the 10 PDBs input to phenix.autoMR vary greatly in molecular weight from their mean value, but the whole is likely an excellent probe for molecular replacement. However, I am stymied by phenix.autoMR: ------------------------------------------------------------------------------------- FATAL RUNTIME ERROR: Molecular weight of /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb (6610.56) deviates more than 20% from the mean (3977.08). This pdb file may contain domains or water not present in the other files. ------------------------------------------------------------------------------------- I understand why this check might be of utility to the unobservant. How can I disable this test? Many thanks, Jim -- James R. Thompson <thompson.james(a)mayo.edu>

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stuck with phenix refine
by intekhab alam 29 Aug '10

29 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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