- phenixbb - phenix-online.org

Re: [phenixbb] pid's from output
by Thomas C. Terwilliger 20 Nov '10

20 Nov '10

Hi Bryan, I added output such as the following to all autosol/autobuild/ligandfit/automr log files: HOST = sigma.lbl.gov HOSTTYPE = x86_64-linux USER = terwill PID = 27371 This will be available starting with tomorrow's PHENIX build. Thanks for suggesting this! -Tom T any way to get pid's of a given phenix process from their output (or any other tricks)? e.g. tried lsof, etc., dug through some title.dat, correlating date.. this would be helpful e.g. when a bunch of autobuilds start after an automr with an expired pid. -Bryan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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phenix refinement question
by Katarina Moravcevic 20 Nov '10

20 Nov '10

Hi all, I have only started using PHENIX and have made an interesting observation. If I run my model through PHENIX refine (individual sites, individual ADPs, occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry values (data is to 1.7A). However, if I now take this refined model and run it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. Can anyone explain why is there such a big difference? Will this be an issue during PDB submission? Any and all comments are appreciated. Thank you all in advance Katarina M.

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phenix.elbow with gamess
by William Scott 19 Nov '10

19 Nov '10

The command phenix.elbow --games --smiles="CCO" now fails (1.61 and most recent nightly), but works in an older version of phenix (1.6). Do I need to change input syntax? (I've tried both with older and more recent 32 and 64-bit gamess). Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ PS: Here is the error output 0:07 WriteGAMESSInput WriteGAMESSInput WriteGAMESSInput WriteGAMESSInput Write 0 -3.5160526786 -17.580263393 1 4.03396746237 20.1698373118 2 -2.978694357 -14.893471785 3 2.92412711501 14.620635575 4 -3.25561740601 -16.2780870301 5 3.2398773487 16.1993867435 [-3.5160526785963961, 4.0339674623667952, -2.9786943570030093, 2.9241271150050951, -3.2556174060111247, 3.2398773486970533] Traceback (most recent call last): File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 1691, in <module> run() File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 1583, in run call_back_function=call_back_function, File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/command_line/builder.py", line 874, in post_process call_back_function=call_back_function, File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/utilities/optimisation_manager.py", line 514, in optimisation_manager function(*args, **kwds) File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/quantum/GAMESSMixins.py", line 403, in WriteGAMESSInput points, outl = get_density_grid(self) File "/usr/local/xtal/phenix-1.6.1-357/elbow/elbow/quantum/GAMESSMixins.py", line 190, in get_density_grid assert 0 AssertionError

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pid's from output
by Bryan Lepore 19 Nov '10

19 Nov '10

any way to get pid's of a given phenix process from their output (or any other tricks)? e.g. tried lsof, etc., dug through some title.dat, correlating date.. this would be helpful e.g. when a bunch of autobuilds start after an automr with an expired pid. -Bryan

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relationship between B factors and Koff
by Sebastiano Pasqualato 19 Nov '10

19 Nov '10

Hi all, I have a crystallographical/biochemical problem, and maybe some of you guys can help me out. We have recently crystallized a protein:protein complex, whose Kd has been measured being ca. 10 uM (both by fluorescence polarization and surface plasmon resonance). Despite the 'decent' affinity, we couldn't purify an homogeneous complex in size exclusion chromatography, even mixing the protein at concentrations up to 80-100 uM each. We explained this behavior by assuming that extremely high Kon/Koff values combine to give this 10 uM affinity, and the high Koff value would account for the dissociation going on during size exclusion chromatography. We have partial evidence for this from the SPR curves, although we haven't actually measured the Kon/Koff values. We eventually managed to solve the crystal structure of the complex by mixing the two proteins (we had to add an excess of one of them to get good diffraction data). Once solved the structure (which makes perfect biological sense and has been validated), we get mean B factors for one of the component (the larger) much lower than those of the other component (the smaller one, which we had in excess). We're talking about 48 Å^2 vs. 75 Å^2. I was wondering if anybody has had some similar cases, or has any hint on the possible relationship it might (or might not) exist between high a Koff value and high B factors (a relationship we are tempted to draw). Thanks in advance, best regards, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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automr/phaser : b-factors
by Bryan Lepore 19 Nov '10

19 Nov '10

does (or can) phaser use the search probe B-factors in any way? -Bryan

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CRYST card being changed
by Nino Campobasso 18 Nov '10

18 Nov '10

Phenix developers, When I run a refinement, it appears that the CRYST card is not being written as expected by programs like pymol and coot. I'll start with a file that has C 1 2 1 and phenix.refine will write out C2 . If I attempt to view symmetry related molecule within coot or pymol, these programs complain that there is no symmetry op. If "fix" the spacegroup in the CRYST line, pymol and coot are happy and generate the related molecules. Best, Nino

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autobuild : rigid?
by Bryan Lepore 18 Nov '10

18 Nov '10

dev-572 my understanding of the autobuild<->refine keyword table on the website is that there's no rigid body available through autobuild - is that right? -Bryan

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reflection file converter
by r n 17 Nov '10

17 Nov '10

Hi I did tried reflection file converter in phenix. I do have the anomalous data, like to keep all anomalous difference and also merged F and FreeR for refinement. Phenix GUI give me an warning message that "File are not suitable for amplitudes change them as F or leave them as Intensities" Also have hard time to convert them in command line, Is there any auto script that can work similar to scaelpack2mtz , which keeps all I+, I- and F , SigF, Rfree for refinement. Converted using Phenix.refine , that keeps separate I+, I- and Rfree+, Rfree-. Thanks ram

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link restraints for modified nucleotides in RNA
by Gerwald Jogl 17 Nov '10

17 Nov '10

Hi All, I am refining several modified nucleotides in ribosomal RNA (N2-methyl-guanosine and similar). While the restraints generation with phenix.reel work quite well, I am unable to get the phosphate oxygen restraints applied properly. Phenix.refine recognizes the links but for some reason the phosphate groups come out quite distorted... For example, angles after refinement: O3 (1) - P (2, modified) - OP2 (2) = 80 deg and O3 (1) - P (2, modified) - OP1 (2) = 127 deg Here is part of the phenix.refine log on reading the coordinates: Chain: "A" Number of atoms: 32526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1513, 32526 Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1, '7M G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1} Classifications: {'undetermined': 11, 'RNA': 1502} Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195} Link IDs: {'rna3p': 1318, 'rna2p': 194} Chain breaks: 1 I am at a loss about how to fix this as all links and restraints seem to be in place. Many thanks for advice, Gerwald

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phaser and automr
by Bryan Lepore 16 Nov '10

16 Nov '10

IIUC, phaser keywords cannot be provided to phenix.automr - is that right? i.e. if that's the case, then i ought to run phenix.phaser. -bryan

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automr : [1] MAP_COEFFS [2] output pdb's of ensemble
by Bryan Lepore 16 Nov '10

16 Nov '10

dev-572 [1] in automr, i do not understand why only the last MR.MAP_COEFFS.n.mtz is written- e.g. i don't get 1-9 if 10 models are requested as output. (MR.[1-n].mtz are written ok). [2] when using an ensemble, i gather that the output is *hardwired* for the best rmsd model - i.e. there are no keywords to write out all parts of the ensemble. (i know i can run pdbset for them, but anyways...) -Bryan

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automr : *refinement* resolution limit keyword?
by Bryan Lepore 16 Nov '10

16 Nov '10

[ dev-572 ] i'm wondering if users can set the *refinement* resolution limits in automr? the webpage suggests this, but it wasn't clear to me. i can set the search resolution fine, however by default as indicated, all data is used - and the only other keyword i see that would at all be relevant is the building resolution. -Bryan

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refine : annealing temperature
by Bryan Lepore 13 Nov '10

13 Nov '10

just wondering if the annealing temperature in phenix is absolutely the same as in cns. -Bryan

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Question about restraints
by Schubert, Carsten [PRDUS] 13 Nov '10

13 Nov '10

Hi, I was wondering what the default values for restraints in reel/elbow represent in terms of 'tightness' for lack of a better word. I am trying to tighten up the geometry of a badly behaving ligand and want to avoid over tightening. What is the consensus out there what kind of ESDs represent a 'loose' 'medium' and 'tight' restraint for bond, angle, dihedral, planar and chiral restraints. Thanks Carsten

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automr : ensemble on command line
by Bryan Lepore 12 Nov '10

12 Nov '10

dev-572 i keep getting this error : The number of entries in identity_list ([80.0, 80.0]) needs to be the same as the number of entries in ensemble_1.coords (1) on the command line, i specify the ensemble as : coords='MR_probe_5_match_to_9.pdb MR_probe_9.pdb' identity='80 80' it gets picked up like this : ... ensembleID = "ensemble_1" copies_to_find = None coords = "MR_probe_5.pdb MR_probe_9.pdb" identity = 80 80 ... i tried using quotes or not, and rmsd. i'm using "\" for the shell - what am i missing here? any clues to look for? -Bryan

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Two Post-Doc opportunities in cell biology and biochemistry in Milan, Italy
by Sebastiano Pasqualato 11 Nov '10

11 Nov '10

Hi all, I'm sending this on behalf of a colleague, so please reply to giorgio.scita(at)ifom-ieo-campus.it if interested. PS: to those concerned, apologies for the double post. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

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phenix.autosol : scala unmerged ok?
by Bryan Lepore 10 Nov '10

10 Nov '10

[ phenix-dev-572 ] i gave autosol unmerged I, SIGI, M/ISYM from scala for a derivative and a native. from the docs, it appears this is automated. but it appears that solve thinks its scalepack_merge, and other things (LAST.LOG) what keywords should i consider here? should i just use scalepack format? -bryan

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autosol/phaser : weak site search and sites
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 is there a keyword to disable phaser's weak site search in an autosol run? it seems that using sites=1, max_single_sites=1, sites_file=one_site.pdb isn't doing it. -Bryan

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autosol : space group
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 i gave P 2 21 21 data to autosol - seems OK until the .pdb's get written out - they have P 21 21 2 instead. will this be of any consequence - or should i use a standard setting? -Bryan

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autosol : crystal info
by Bryan Lepore 10 Nov '10

10 Nov '10

dev-572 i gather that a .params for isomorphous replacement gets one cell in the crystal_info scope? -bryan

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C and C++
by Hena Dutta 09 Nov '10

09 Nov '10

Dear Members, Sorry for unrelated questions. I thought some of you might have information could be helpful for me. Is there any free website for learning C and C++? Thanks... Hena

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geometry
by Jianghai Zhu 09 Nov '10

09 Nov '10

Hi all, I am refining a 2.75 A structure. The wxc_scale is 0.02, optimize_wxc is false. But the geometry I got doesn't make sense at all. Any explanations? ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 0.617 0.004 0.039 14.275 0.003 4.123 5.8886e-02 1_bss: 0.617 0.004 0.039 14.275 0.003 4.123 5.8886e-02 1_xyz: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 1_adp: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 2_bss: 3.391 0.059 0.209 16.068 0.010 4.114 1.3055e+00 2_xyz: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 2_adp: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 3_bss: 2.435 0.032 0.180 15.961 0.007 4.114 5.4206e-01 3_xyz: 2.139 0.025 0.191 15.477 0.007 4.114 3.7907e-01 3_adp: 2.139 0.025 0.191 15.477 0.007 4.114 3.7907e-01 ------------------------------------------------------------------------ Thanks. -- Jianghai

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Re: [phenixbb] question on the missing fobs filled maps
by Alexandre OURJOUMTSEV 09 Nov '10

09 Nov '10

Hello, Continuing and confirmating Pavel's last comments: yes, we saw a number of practical cases when non-uniformly distributed missed data, even a small percent, caused great map distortions (some example are listed in our manuscript recently submitted to J.Appl.Cryst). To track this situation, recently we have developed a small python-based program that starting from your MTZ file searches for connected regions of such unmeasured reflections, gives their characteristics and visualizes the regions on the user's request. Presence of such regions may make your maps ugly even when the phases are perfect. For an official release when ready the program will be available at the Web site of the institute; for a time being if you want to test the current version please send me a mail to sacha(a)igbmc.fr With best regards, Sacha Urzhumtsev -----Message d'origine----- De : phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] De la part de Pavel Afonine Hi Fengyun, > I am interesting in that at what completeness of the dataset, will one > use the missing fobs filled map for model building confidently without > too much bias included? I'm not aware of any systematic study on this matter, although at some point I reviewed the available literature. There are numerous examples of how the data incompleteness distorts the map, and literature that discusses this. Interestingly, sometimes much smaller amount of systematically missing reflections, such as plane or cone in reciprocal space, may have much drastic effect than a larger amount of randomly missing data (if you are "lucky" enough it can mask entire structural domain).

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moving user home directories
by Ben Eisenbraun 09 Nov '10

09 Nov '10

Hi PHENIXians, Our local sysadmins moved everyone's home directory from /nfs/home/foo to /nfs/userdocs/home/foo, and it appears to have broken most people's PHENIX projects. Is there a straightforward way to fix this? Poking around in the ~/.phenix/project_db.pkl files, I can see the old paths, but I'm not exactly sure how to rewrite. My brute force attempt with sed was unsuccssful. Thanks. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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