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Advice about phasing procedure and phase extension in AutoSol-AutoBuild
by Schubert, Carsten [PRDUS] 08 Nov '07

08 Nov '07

Hi, I am trying to bootstrap my way into a couple of weak derivatives using a combination of Solve and the AutoSol and AutoBuild wizards. I have probably one or two fairly weak diffracting derivatives (~3A) with low FOMs (~0.3) from Solve, the native extend to ~2.A. I have a couple of questions about how to best proceed with the phasing procedure using either the wizards or a Solve/Resolve combination. 1. can I input known HA-positions into the AutoSol wizard to help Hyss find other positions? Does Hyss actually eliminate bogus sites? Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a B-factor of one, but does not toss them. How does Hyss handle this situation? 2. What is the best way to handle phase extension in the Wizards, how would one go about this? I would like to fine-tune the resolution steps myself as not to jump to far out to higher resolution. 3. What quality indicators should I look at? A couple of FOMs in the resolve runs were in the region of 0.7, but the maps were not interpretable and resolve failed to build anything. Anything else I should look at? Thanks Carsten

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Re: [phenixbb] autobuild 'hires_file'->now FreeR flags, merging, ...
by Tom Terwilliger 07 Nov '07

07 Nov '07

Hi Bryan, >On Tue, 6 Nov 2007, Thomas C. Terwilliger wrote: > > The problem is in that version of phenix. I'm sorry about that! Can you > >that solved it, thanks. Oh good. > >> [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag > >> 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases > >> will be extended to a high resolution limit as found in w1.sca? (vide > >> infra) > > > > Yes, that is correct. > >ok, then i have to ask - is phenix merging each reflection? i.e, i >wouldn't want to do this w/ a derivative and hi-res native, right? Yes, it is merging in each reflection, if I understand the question. Yes, you might do it with phases from a native+derivative and a hi-res native. (We're only talking about doing this in autobuild, after you have "experimental" phases from something.) -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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error message running example
by Kairies, Norman 07 Nov '07

07 Nov '07

Hi - I tried to run the example: phenix.run_example gene-5-mad However, it stopped, with following error messages: Done with gene-5-mad ...Your results are in the directory: gene-5-mad/AutoSol_run_1_ Missing the summary file: gene-5-mad/AutoSol_run_1_/ Something did not work properly...not all output files produced and the LAST.LOG reports: ************************************************************************ *** 6769 SOLVE STATUS 07-nov-07 12:47:15 6770 6771 DATASET TITLE: SOLVE 07-Nov-07 STATUS 6772 STATUS: UNABLE TO FIND UNIQUE NAME FOR SCRATCH 6773 ------------------------------------------------------------------------ --- 6774 Sorry -- ERROR ENDING. SEE the end of your log file or output STATUS 6775 and solve.log 6776 for more information STATUS Any idea what is going wrong? (phenix version 1.3 beta rc4, 64bit computer, 2 dual core proc.) Many thanks, Norman

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autobuild 'hires_file'
by Bryan W. Lepore 07 Nov '07

07 Nov '07

i have phenix 2007_08_18_1856, (and i think latest cci apps). i have a jumble of questions, i'll try step by step: [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra) [1 B] can the labels be the same as the 'other' data (the documentation suggests this)? i have tried a few things like : phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt ... and i see Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat'] ... which is good, but the job promptly fails with this cryptic (to me) error message: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ ... (google:all_input_hires_labels and looking through docs quick didn't find it) -bryan

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PDB deposition of tls refined structure
by Rene Jorgensen 01 Nov '07

01 Nov '07

Dear phenix users, I am about to deposit a 2.5A structure at the PDB. The structure has been refined using phenix.refine with strategy=tls+individual_sites +individual_adp, which actually works very well but (because of the tls refinement) also results in the output of ANISOU records for the atoms in the PDB file. When using PDB_extract during the PDB submission process the ANISOU record is picked up as regular anisotropic refinement although the resolution is too low for that. Should I just accept it and leave it as it is or should I correct the info in the Auto Dep Input Tool (ADIT) to isotropic with just the regular b-factor values? Thanks in advance, Rene Jorgensen

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Pango
by Frank von Delft 01 Nov '07

01 Nov '07

Hi, I just installed the latest phenix version (long overdue), and it burps with the following when I try to run the GUI. Looks like an absolute path was left lying around, no? Cheers phx ---------------------------------------------------- Running the PHENIX GUI with /usr/local/phenix/1.3b/phenix-1.3b/build/intel-linux-2.4/base/bin/python PHENIX distribution located in /usr/local/phenix/1.3b/phenix-1.3b/phenix Shell variable SSH_PATH not set Variable PYMOL_PATH set to /usr/local/phenix/1.3b/phenix-1.3b/pymol Shell variable RSH_PATH not set (python:31886): Pango-WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: '/net/ribbon/scratch1/phenix/phenix-1.3b/build/intel-linux-2.4/base/etc/pango/pango.modules' You should create this file by running pango-querymodules. (python:31886): Pango-WARNING **: pango_shape called with bad font, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_glyph_extents called with null font argument, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_metrics called with null font argument, expect ugly output (python:31886): Pango-WARNING **: _pango_cairo_font_install called with bad font, expect ugly output ----------------------------------------------------

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Re: [phenixbb] lower limits on grid spacing/binning
by Ralf W. Grosse-Kunstleve 31 Oct '07

31 Oct '07

Probably, the original poster already got more than he bargained for, but for the records, a few more comments: > All FFT based structure factor programs require that the sampling > rates along each axis be even. I don't think this is true, unless I'm misunderstanding what "sampling rate" means. The FFT in phenix is based on FFTPACK (written in the 80s) which works for any number of grid points. FFTw also supports arbitrary gridding. > They may have other required factors > depending on the space group, but they will be happy to inform you > if you make a choice it doesn't like. They are also more efficient > when the prime factors of the sampling rates are small numbers. Try > to stick with multiples of 2,3, and 5 if possible. That's good advice. FFTPACK is fastest for transform sizes that are multiples of 2,3,4 and 5. The map calculation algorithms in phenix automatically take this into account. > All FFT programs will fail if you > sample your map courser than twice that frequency, as SFALL did for > you. This may be true for SFALL, but not for the FFT algorithms in the phenix libraries ($PHENIX/cctbx/include/cctbx/maptbx/structure_factors.h). The critical reference is: David A. Langs (2002), J. Appl. Cryst. 35, 505. As short as it is, this was an incredibly important paper. In retrospect, it is amazing that it took so long for someone to discover the trick. Ralf

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lower limits on grid spacing/binning
by Terry Lang 30 Oct '07

30 Oct '07

Hey Everyone, I have been told by several crystallographers that the general rule of thumb for grid spacing when generating a map is one third the resolution (eg If your crystal structure has a resolution of 1.2 A, your grid spacing should be 0.4). Is there a mathematical reason why this ratio should be maintained or is this simply a holdover from slower computers with lower memory? More importantly for my application, is there a lower limit on how fine the grid spacing can be? In other words, is there a lower limit at which one is oversampling the data for a particular resolution? Any information and/or references would be greatly appreciated. Sincerely, Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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linking residues question
by Crystal K. Chuang 26 Oct '07

26 Oct '07

Hello all, I was wondering if there is a tool in RESOLVE that, when used through PHENIX, links up individual chains of residues and ties in symmetry related fragments so that, as a result, packs everything together to generate more of a globular unit? Many thanks, -Crystal

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NCS interpretation
by Claudia Scotti 25 Oct '07

25 Oct '07

Dear list, I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules (2 A resolution). The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97 90.04 89.97), but only P1 + twinning worked for MR and for refining the structure (Rfree=0.22; Rcryst=0.18). The crystal simulated a P222 space group (the best seemed to be P21212), so I'd expect NCS axis parallel to . Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators (see ouput below). I've read the manual, but I'm nevertheless finding it difficult to " see" the NCS axis. Any suggestions, please, on how to interpret the output, please, and "draw" the axis or on any alternatives on how to proceed? Many many thanks and a huge apology for the naive question (this is only my third strutcure...). Claudia --------------------------------------------------------------------------- # simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type simple_ncs_from_pdb --help for help Parameters used for simple_ncs_from_pdb: find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']] Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148, 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148, 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]] GROUP 1 Summary of NCS group with 8 operators: ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]]]] RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59 Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213, 211] Source of NCS info: sortwaterxyzout.pdb OPERATOR 1 CENTER: 19.3475 -10.7352 7.9738 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 53.8092 24.2127 11.0612 ROTA 1: 0.9998 0.0043 -0.0190 ROTA 2: 0.0045 -0.9999 0.0114 ROTA 3: -0.0190 -0.0115 -0.9998 TRANS: -34.3014 13.1765 20.2795 OPERATOR 3 CENTER: 55.6227 -15.2644 6.2461 ROTA 1: -0.9928 -0.0019 -0.1198 ROTA 2: -0.0045 -0.9986 0.0530 ROTA 3: -0.1197 0.0532 0.9914 TRANS: 75.3327 -25.9880 9.2016 OPERATOR 4 CENTER: 21.4489 28.7297 12.8232 ROTA 1: -0.9923 0.0066 0.1235 ROTA 2: -0.0001 0.9985 -0.0545 ROTA 3: -0.1236 -0.0541 -0.9909 TRANS: 38.7377 -38.6213 24.9897 OPERATOR 5 CENTER: 33.2332 16.3336 52.0552 ROTA 1: 0.9959 0.0207 -0.0884 ROTA 2: -0.0168 0.9988 0.0450 ROTA 3: 0.0892 -0.0433 0.9951 TRANS: -9.4176 -28.8046 -46.0499 OPERATOR 6 CENTER: 35.8216 -23.2140 56.1297 ROTA 1: -0.9985 -0.0249 -0.0490 ROTA 2: -0.0273 0.9985 0.0479 ROTA 3: 0.0477 0.0492 -0.9976 TRANS: 57.2101 10.9031 63.4545 OPERATOR 7 CENTER: 70.2188 11.8599 54.2973 ROTA 1: -0.9987 0.0207 0.0473 ROTA 2: -0.0234 -0.9981 -0.0569 ROTA 3: 0.0460 -0.0580 0.9973 TRANS: 86.6599 5.8364 -48.7180 OPERATOR 8 CENTER: 67.5293 -27.9008 58.5120 ROTA 1: 0.9959 -0.0146 0.0888 ROTA 2: -0.0120 -0.9995 -0.0303 ROTA 3: 0.0892 0.0291 -0.9956 TRANS: -53.5269 -35.9247 61.0251 NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_spec Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE

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