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sculptor : "Wrong alignment format:"
by Bryan Lepore 29 Nov '10

29 Nov '10

(starting a new thread?) trouble with alignment format. tried this : fubar.fas : Sorry: Unknown file(s): fubar.fas fubar.fasta : Sorry: Wrong alignment format: fubar.fasta i compared to one that worked yesterday and its not obvious : first sequence is the target, the pdb sequence is in there (somewhere), i changed a ">sp" to ">gi".... if anyone knows what i'm missing here,... -Bryan

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International Conference on Structural Genomics May 10-14, 2011, Toronto -- registration now open
by Tom Terwilliger 29 Nov '10

29 Nov '10

Dear Colleagues, We are pleased to announce that registration is now open for the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. A substantial number of short talks will be selected from submitted poster abstracts. Also, a limited number of student travel fellowships will be available for travel to this meeting. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Dear all! How to refine occupancies of mutually dependent structural fragments found in alternate conformations, but not consecutive in a sequence? E.g. I want to refine occupancies of two alternate conformations of residues 30 and 451 (see below the corresponding parts of a PDB file). Because of the nature of the structural disorder, an occupancy for altLoc A should be strictly the same in both fragments - the same is valid for altLoc B. Of course, the sum of occupancies for altLoc A and B should add up to 1. Thanks for your suggestions, Dalibor Milic ... ATOM 376 N AGLU A 30 23.241 86.975 31.961 0.52 17.13 N ATOM 377 N BGLU A 30 18.971 88.677 32.817 0.48 9.05 N ATOM 378 CA AGLU A 30 23.240 85.507 31.907 0.52 18.89 C ATOM 379 CA BGLU A 30 19.108 87.234 32.991 0.48 10.00 C ATOM 380 CB AGLU A 30 21.848 84.946 32.256 0.52 18.78 C ATOM 381 CB BGLU A 30 17.727 86.562 33.046 0.48 11.01 C ATOM 382 CG AGLU A 30 21.247 85.562 33.524 0.52 26.38 C ATOM 383 CG BGLU A 30 16.935 87.037 34.275 0.48 19.26 C ATOM 384 CD AGLU A 30 20.264 84.659 34.277 0.52 33.36 C ATOM 385 CD BGLU A 30 15.694 86.223 34.542 0.48 26.60 C ATOM 386 OE1AGLU A 30 19.437 83.968 33.620 0.52 31.85 O ATOM 387 OE1BGLU A 30 15.401 85.288 33.762 0.48 33.05 O ATOM 388 OE2AGLU A 30 20.310 84.678 35.535 0.52 29.12 O ATOM 389 OE2BGLU A 30 15.007 86.527 35.538 0.48 30.95 O ATOM 390 C AGLU A 30 23.750 84.946 30.575 0.52 18.22 C ATOM 391 C BGLU A 30 19.976 86.652 31.877 0.48 10.17 C ATOM 392 O AGLU A 30 24.319 83.853 30.534 0.52 19.40 O ATOM 393 O BGLU A 30 20.621 85.606 32.059 0.48 10.67 O ... ATOM 4627 N AALA A 451 31.047 82.837 22.335 0.52 18.30 N ATOM 4628 N BALA A 451 29.107 84.432 26.354 0.48 9.81 N ATOM 4629 CA AALA A 451 31.958 83.502 23.284 0.52 18.73 C ATOM 4630 CA BALA A 451 29.655 85.424 27.274 0.48 9.73 C ATOM 4631 CB AALA A 451 32.880 84.486 22.541 0.52 20.38 C ATOM 4632 CB BALA A 451 30.469 86.474 26.478 0.48 11.60 C ATOM 4633 C AALA A 451 31.176 84.206 24.406 0.52 18.79 C ATOM 4634 C BALA A 451 28.556 86.128 28.089 0.48 6.84 C ATOM 4635 O AALA A 451 30.019 84.593 24.197 0.52 18.25 O ATOM 4636 O BALA A 451 27.441 86.357 27.604 0.48 6.81 O ... -- Dalibor Milic, Dr. Sc. Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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Re: [phenixbb] occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Just an additional comment to my previous e-mail: the refined final value of occupancies in the expression occupancy(AGLU A 30) = occupancy(BGLU A 30) = occupancy(AALA A 451) = occupancy(BALA A 451) were not equal to 0.50 and I got occupancy(AGLU A 30) + occupancy(BGLU A 30) = occupancy(AALA A 451) + occupancy(BALA A 451) < 1.00. Regards, Dalibor -- Dalibor Milic Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

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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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