- phenixbb - phenix-online.org

Re: [phenixbb] phenix.refine crash
by Ralf W. Grosse-Kunstleve 25 Feb '07

25 Feb '07

> Anyone has any idea what is happening? Thanks. It is a bug that we've fixed already. We will release a new cci apps in the next couple of days that will include the fix. In the meantime, could you try removing the ANISOU cards (grep -v ANISOU xxx.pdb)? I think that should work around the problem. Ralf

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Re: [phenixbb] input HA
by Tom Terwilliger 13 Feb '07

13 Feb '07

Hi Morton, I'm sorry to make it difficult! Here are 2 formats that should work: 1. PDB format (I'm not sure why the one from cns failed...can you send me a line or two from that so I can make it work?): HETATM 1 SE SE 3 73.920 0.324 3.857 0.92 54.60 Se HETATM 2 SE SE 4 39.591 8.262 2.158 0.55 60.00 Se 2. Plain fractional xyz, with or without the word "xyz". For example see: $PHENIX/examples/gene-5-mad/sites.xyz : xyz 0.0271 0.8074 0.0657 xyz 0.0239 0.0116 -0.0965 Please let me know if this doesn't do it! -Tom T At 03:52 AM 2/13/2007, Morten Grøftehauge wrote: >Ok, I give up. > >What is the correct format for a heavy atom file >for AutoSOL? I've tried both the outputs from >FFT, CNS pdbs and sdbs and I've tried just >putting them on a line like you do for SHARP: >ATOM Br - 0.0120 0.5731 0.2740 >but none of them are accepted by Phenix. >Any help please? > >-- >Morten K Grøftehauge >PhD student >Department of Molecular Biology >Gustav Wieds Vej 10 C >8000 Aarhus C - Denmark >Phone: +45 89 42 50 10 >Fax: +45 86 12 31 78 ><http://www.bioxray.dk>www.bioxray.dk > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb 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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input HA
by Morten Grøftehauge 13 Feb '07

13 Feb '07

Ok, I give up. What is the correct format for a heavy atom file for AutoSOL? I've tried both the outputs from FFT, CNS pdbs and sdbs and I've tried just putting them on a line like you do for SHARP: ATOM Br -0.0120 0.5731 0.2740 but none of them are accepted by Phenix. Any help please? -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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CCI Apps
by Noinaj 26 Jan '07

26 Jan '07

Hi, Quick question. I am trying to refine occupancy of a ligand and was attempting to do this using the method outlined under the CCI Apps documentation for phenix.refine. a.. Refinement of one occupancy factor per selected group of atoms (group occupancy refinement): % phenix.refine data.hkl model.pdb strategy=group_occupancies \ refine.occupancies.group="chain A and resid 1"Yet, when I type the commands, I keep getting an error saying that something is wrong with my commands: strategy, group, etc. I have not (at least I don't recall) loading the updated CCI Apps and only have what was installed with Phenix 1.24b installation. Am I doing something wrong here or do I need to update the CCI Apps? Thanks in advance for all feedback! Cheers, Nick ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 noinaj(a)uky.edu www.noinaj.com

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New CCI Apps
by Ralf W. Grosse-Kunstleve 25 Jan '07

25 Jan '07

On behalf of the Phenix development team I'm pleased to announce the release of a new CCI Apps version: http://phenix-online.org/download/cci_apps/ Version 2007_01_24_2154 Simultaneous use of NCS restraints and automatic water picking. Individual anisotropic ADP restraints (similar to SHELXL SIMU). Bug fix in processing of multiple apply_cif_link blocks applied to the same residue. Send bug reports to: bugs(a)phenix-online.org For help write to: help(a)phenix-online.org

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questions
by Jianghai Zhu 17 Jan '07

17 Jan '07

Hi, Got some questions in using phenix.refine. 1) Can phenix.refine use the ligand library generated by refmac5? 2) How do I use elbow to generate the ligand library when I have more than one kind of ligands? When I used --residue=xxx more than once, elbow will only generated library for the last ligand. If I use elbow multiple times to generate multiple libraries, how do I read the libraries in? Should I combine them to one file? 3) When I ran phenix.refine, I found the following message in the log. Number of residues, atoms: 32, 418 Unusual residues: {'NAG': 22, 'MAN': 10} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 32 Number of residues, atoms: 18, 28 Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14} Classifications: {'undetermined': 18} Link IDs: {None: 17} I already gave the cif library for NAG. Looks like nothing happened. How come phenix.refine doesn't recognize Glycerol, Mg, and Ca? 4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong? Thanks. Jianghai

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Re: [phenixbb] phenix.hyss
by Ralf W. Grosse-Kunstleve 17 Jan '07

17 Jan '07

Hi Jianghai, I think the large memory consumption is due to the large number of triplet phase relations. Using the --real_space_squaring option may help. > The MAD data only goes to 4 A. I tried SOLVE and based on the CC > table output from SOLVE, the anomalous signal goes to 4.3 A. I > believe the cut of CC in SOLVE is 0.3. Unfortunately, the native > data is not isomorphous. Finding 50 Se given only 4.3 A resolution is difficult. I'm sorry to say I'm not very hopeful, but I'd try all tools out there. I'd also play with the resolution cutoff. hyss used 4 A in your case. I'd try 4.5 and maybe even all cutoffs 4.4, 4.3, 4.2, 4.1 if you can afford the CPU time, with --real_space_squaring first, without it if nothing worked still. Another question is the space group. You cannot distinguish I222 and I212121 from the systematic absences. Are you certain it is I212121? To find a cluster, lower the resolution significantly. I've had success with 6 A cutoff (--resolution=6). The atom type doesn't really matter, Ta should be fine. If it works, hyss will give you atoms around the centers of the clusters. You have to fit the whole cluster yourself. I'm not sure about the best approach for this (inspecting the map with coot and place the cluster manually?). Maybe someone else can help? How many clusters do you expect? In general, the more you expect the more data you need. I.e. a 6 A cutoff may work for finding a couple of sites, but for say 10 sites you'd need 5 A. -- These numbers are just to convey the idea. What works exactly depends highly on the available data. Hope this helps. Cheers, Ralf

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Re: [phenixbb] phenix.hyss
by Ralf W. Grosse-Kunstleve 17 Jan '07

17 Jan '07

Hi Jianghai, phenix.hyss isn't normally using that much memory. To help me understand what is happening, could you please email me the complete output (I will keep it confidential if you email to rwgk(a)cci.lbl.gov directly). Thanks! Ralf

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mmtbx.twin_map_utils utility
by Jorge Iulek 03 Jan '07

03 Jan '07

Hallo, This must be a naive question, but following Dr. Zwart's previous post and as I found in the web (http://www.phenix-online.org/phenix_wiki/mmtbx.twin_map_utils) this should be a utility to calculate a detwinned map. I just installed phenix and everything seemed to be fine during installation. But, where is this utility ? I cannot find it. Thanks, *********************************************************************** Prof. Jorge Iulek, Ph. D. Protein Purification and 3D Structure Determination Group State University of Ponta Grossa Telephone: ++ 55 - 42 - 3220-3062 Fax: ++ 55 - 42 - 3220-3262 iulek(a)uepg.br iulek(a)interponta.com.br *********************************************************************** !!!!!!!!!!!!!!!!!!!!!!!!!!Hi Brian, There are map utilities for twinned data indeed. mmtbx.twin_map_utils carries out refinement of the overall, anisotropic scale, bulk solvent parameters and twin fraction. It spits out the maps afterwards. Unfortunately, refniement against twinned data is not yet fully implemented in phenix.refine but we are working on that. HTH Peter > i see there are map utilities for twinned data. > > but before i go try refinement of a twin - will phenix.refine refine > against twinned data? > > if so, is alpha determined each time, thus, alpha is not specified > in the > .def? > > -bryan > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- Esta mensagem foi verificada pelo sistema de antivírus e acredita-se estar livre de perigo.

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full omit maps
by Miguel Ortiz Lombardia 29 Dec '06

29 Dec '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello everyone, I'm trying to obtain a full omit map as it was described by Tom Terwilliger in a previous post: http://www.phenix-online.org/pipermail/phenixbb/2006-October/000108.html However, when I run the AutoBuild strategy asking for no rebuilding / no refinement all I get in the FULL_OMIT directory is a collection of pdb files named 'overall_best.pdb_OMIT_REGION_x' where 'x' correspond to each of the 'omit regions'. But I get no 'resolve_composite_map.mtz' whatsoever. Surely I'm missing something. I would appreciate your guidance. Have all of you an excellent year 2007! All the best, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFFlNB7F6oOrDvhbQIRAuBpAJwK4/+sj+5PowBBIvNVE0Tvyin7wwCdHFOS QHrtAM+9afN+2RTGshFB8KU= =IXga -----END PGP SIGNATURE-----

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