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question on the weight for adp
by fn1＠rice.edu 01 Oct '10

01 Oct '10

Hi everyone, I have some questions the weight for adp. My case is that some part of the model will be refined to large B values (about 100) if the default value of wxu_scale (1.0) is used. The other part of the model will have average B value of about 40, which the wilson B is about 35. The corresponding 2FOFC map has very poor density for the region with large B values. If the value of wxu_scale set to be 0.1, that part with large B will be refined to about 80 for B. The corresponding 2FOFC map has some better (but not good enough) density for this region. My question is that can I keep the wxu_scale at the small value for the refinement? Or finally do I need to loose this value? Thanks! Fengyun

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Seeking Postdoctoral Researcher
by Francois Berenger 30 Sep '10

30 Sep '10

Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral Researchers Job description: We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, and structure-based drug design. Our ability to predict the structure of proteins from their primary sequences will greatly facilitate our understanding of the important biological functions that proteins play in their host systems. The 3D structure information will also facilitate the rationale design of drugs for the treatment of various diseases with unmet medical needs. Qualifications: This position requires a PhD in areas related to biophysics, biochemistry, computational chemistry, bioinformatics, or structural biology with experience in employing computational tools to solve biological or chemical problems. Experiences in protein folding, protein structure prediction, protein structure analysis, protein crystallography, or structure-based drugs are highly desired. Proficiency in object-oriented programming such as C++, Java, scripting languages such as Python, Perl are also desired. Experiences in high performance computing, network computing, or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment will be international and hence communication in English is encouraged. The complete job ad, as well as how to apply can be viewed here: http://www.riken.jp/engn/r-world/info/recruit/k100817_s_asi.html Best regards, Francois.

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Ligand restraints editing with REEL -summary
by Joseph Brock 29 Sep '10

29 Sep '10

Hi all, I just wanted to post a quick summary of how my problem was resolved. I later realised that the 'native glutahione' molecule I was transferring ligand restraints from was actually produced by eLBOW released under the Phenix package v1.4, and was therefore defined differently to those restraints created by v1.6.4-486. I was advised by Nigel (author of eLBOW and REEL) to download the latest nightly build (dev-541) and create a clean subdirectory. Copying my model.pdb and data.mtz file into this, running phenix.ready_set on these files and running phenix.refine with the resulting .pdb and .cif files, resulted in a ligand that was correctly restrained to refine into the density extremely well. Hope this is of help to anyone with a similar problem. Cheers, Joe. > From: phenixbb-request(a)phenix-online.org > Subject: phenixbb Digest, Vol 58, Issue 18 > To: phenixbb(a)phenix-online.org > Date: Sat, 18 Sep 2010 12:00:01 -0700 > > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Ligand restraints editing with REEL (Joseph Brock) > 2. Re: Ligand restraints editing with REEL (Ralf W. Grosse-Kunstleve) > 3. Resolve NCS masks (Florian Schmitzberger) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Sep 2010 08:09:23 +0000 > From: Joseph Brock <joeylives2ride(a)hotmail.com> > To: <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Ligand restraints editing with REEL > Message-ID: <SNT120-W580E16EA4DC524ED59A3209B7C0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. > > I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). > > I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. > > Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. > > Thanks so much in advance. > > Cheers, > > -Joe. > > >

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mlhl refinement
by Florian Schmitzberger 28 Sep '10

28 Sep '10

Dear All, I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine (phenix.refine) a model with MLHL target and experimental phase information. Strange thing is when I load the mtz file, as written out from Phenix Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix refine GUI does not seem to any phase information. Only picks up FP and SIGFP labels; but not the Hendrickson-Lattman coefficients, which are present. The following message comes up when I try to chose mlhl refinement: " You have selected 'mlhl' as the refinement target, but no experimental phases were supplied. If you wish to use phase restraints in refinement, please add or select experimental phases, or choose another target function". I guess it is not such a major problem as I can save the .eff file and manually edit it to include the HL coefficients and then run Phenix (as long as Phenix then recognizes them from the mtz file). I would also like to refine f' and f'', as the data are from a selenomethionine derivatized protein. From what I can see the default in Phenix.Autosol seems to be not to keep the F+/- and Dano labels for the output mtz file? So I suppose I do need to provide the initial mtz file or is there a way to change the output options for the coefficients in Phenix Autosol? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?
by Rojan Shrestha 28 Sep '10

28 Sep '10

Hello: I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain. Thanks Regards, Rojan

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CCP4 Study Weekend 2011: "Model Building and Refinement and Validation"
by ronan.keegan＠stfc.ac.uk 24 Sep '10

24 Sep '10

Dear All, We're pleased to announce that registration for this coming January's CCP4 Study Weekend meeting is now open. The meeting will take place from January 5th to 7th, 2011 at University of Warwick in the UK. The topic of the meeting will be "Model building and Refinement and Validation". This year's organisers, Roberto Steiner and Bernhard Rupp, have arranged the usual mix of interesting and stimulating lectures from some of the foremost speakers in the field along with the opportunity to see demonstrations of the latest software developments from CCP4 during the lunch-time bytes sessions. For more information on the program and registration details please go to the Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, The CCP4 team -- Scanned by iCritical.

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separate amino acid chains
by Florian Schmitzberger 23 Sep '10

23 Sep '10

Dear All, Quick question regarding the handling of different amino acid chains in the Phenix Autobuild GUI. From the manual I understand that different amino acid chains are separated by > ? I pasted the my amino acid chains in the GUI separated with > ; I don't think in my case Phenix recognizes the different chains as such, but as one contiguous protein. Am I missing anything obvious? Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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autobuild : use of ncs
by Lepore, Bryan 22 Sep '10

22 Sep '10

i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B. however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used. so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb? -bryan

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PDB Tools and CNS formatted structure factors
by Joseph Noel 22 Sep '10

22 Sep '10

Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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FYI : autobuild : "refine_pdb_in.mtz is missing" etc.
by Lepore, Bryan 22 Sep '10

22 Sep '10

here's a google-able post of a *solved problem* for the archive : phenix 1.6.4-486 (latest official release as of 21sep2010) building ends (FINISHED) with error messages (see below). some associated job setup details : phenix.autobuild with CL flag refine_eff_file_list=my_refinement_params.eff cartesian or torsion annealing, or start_temperature work OK in building/refinement. two segid's in .pdb, one chain id etc. SOLUTION : use the latest build. i used phenix-dev-533 GNU/Linux 32-bit. and thanks especially to Tom Terwilliger for the solution. [key error messages]: Failed to carry out AutoBuild_multiple_models: Sorry a subprocess has failed... Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz is missing...

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