November 2010 - phenixbb - phenix-online.org

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 09 Nov '10

09 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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