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phenix.refine problems with my pdb
by Matthew Bowler 15 Mar '07

15 Mar '07

Dear All, I am trying to run phenix.refine but I keep getting the message: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 308 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions. I have run my ligands through elbow and used the output .cif but I still get the same message. I can find no info on this problem in the manual or the BB, can anyone help? Thanks in advance, yours, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

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Two groups per residue and multiple trajectories for simulated annealing
by Stephen Graham 02 Mar '07

02 Mar '07

Hi all, I am taking my first tentative steps into the world of phenix.refine with a somewhat problematic 3 A data set and I had a few questions that Google couldn't answer. I am running phenix.refine version 1.24.1b (intel-linux-2.6) from the command line. Firstly, is it possible to do 'grouped' adp refinement with 2 groups per residue (like the good old bgroup.inp of CNS)? Secondly, is it possible to specify multiple starting trajectories for simulated annealing? I often find it handy to do 10 runs of simulated annealing and overlay the output co-ordinates to see where the 'wobbly' bits are. Lastly, can the latest version of phenix.refine do SA omit maps? Thanks, Stephen P.S. My .def file is the default (from phenix.refine --dry-run) w/ the following changes: 86,87c86,87 < refine_adp_individual = True < refine_adp_group = False --- > refine_adp_individual = False > refine_adp_group = True 92c92 < simulated_annealing = False --- > simulated_annealing = True -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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Phased anomalous difference map
by Luca Jovine 28 Feb '07

28 Feb '07

Hello, Is it possible to calculate a phased anomalous difference map with phenix.refine? Thanks, Luca

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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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