- phenixbb - phenix-online.org

same origin
by r n 24 Nov '10

24 Nov '10

Hi all I wanted to compare the two models from two data set. I want the MR replacement in same origin to compare their them with respect to the map and model. I tried reforigin in ccp4 , it gave me some error , that I am not aware or not clear. I did tried overlay the two model and rfree is going up. Most likely different hands, so Is there any way to compare the two model and data and modify them in Phenix either reindex or shift the model origin to same in all cases. Thought phenix.xmanip could help, not seen any option to do it command line or in the GUI. I did tried def file, but phenix.xmanip params.def , it complains me that unknown file or keyword? any help will be appreciated. Thanks ram

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sculptor
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-572 I am checking out sculptor, looks pretty cool, but I provided what i thought was a clustal format alignment to sculptor using --verbose, and it reports "Sorry: Wrong alignment format:" that's it. sounds like user error, but i'm not sure where to proceed next. i tried mafft and clustalw2 output for this. a sample of a bit of the top of the .aln is below. -Bryan p.s: shouldn't readseq convert it to .pir? that'd be code 14 PIR/CODATA? CLUSTAL format alignment by MAFFT L-INS-i (v6.833b) gi|16132042|ref --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI gi|157163695|re --ANVRLQVEGLSGQLEKNVRAQLSTIESDEVTPDRRFRARVDDAIREGLKALGYYQPTI

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sculptor : alternate conformations
by Bryan Lepore 22 Nov '10

22 Nov '10

dev-586 i'll probably try this anyways, but what is the advice on alternate conformations with sculptor? -Bryan

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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 18 Nov '10

18 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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