March 2008 - phenixbb - phenix-online.org

autosol output to electron density figure in pymol
by shivesh kumar 02 May '08

02 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

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question about refinement in a SAD data set
by Pascal EGEA 31 Mar '08

31 Mar '08

Dear All, I am trying to refine a seleno met structures at 2.2 Ang resolution I used Auto_Sol and Auto_Build and it worked great since it found the 4 semets with occupancies of about 0.85 to 0.95. and most of the model was built. Phenix generated an exptl_fp_phases.mtz with the Rfree flag. so far so good. I have a couple of questions because I am not quite to understand what phenix.refine is doing at this stage? 1- If I refine using the experimental phases mtz file generated by the auto_sol run, the occupancies for the seleniums change quite a bit and they drop to 0.75-0.80 and that does not sound right to me? What am I doing wrong? should I fix occupancies for the seleniums to the values evaluated at the end of the auto_build run (Rfree=27/ Rfac=24?) 2- This experimental phases mtz file contains FP and the HL coefficients for the phases but there are no more anomalous differences. If I try to refine f' and f" using it, Phenix tells me that there is no anomalous information contained in this file. So how do you refine f' and f"? and what is the practical reason for this AutoSol generated mtz file to not contain the anomalous differences that were used to locate the seleniums. Thanks in advance for the explanation Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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Getting Residual Bs
by Frank von Delft 30 Mar '08

30 Mar '08

Hi Pavel, picking up on your point earlier: > and that there are tools available from both ends (phenix, ccp4) to easily > go from partial to total and back. What *is* the tool in phenix to from total to partial? I suspect it's one of the phenix.pdbtools adp commands, but the documentation is a bit sparse on that program. Cheers phx P.S. Pavel, despite my rant today: great program! :-)

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Re: [phenixbb] refmac,tlsanl vs TLS, B and anisou
by Paul Adams 30 Mar '08

30 Mar '08

Some comments: - We (the PHENIX developers) are working with the PDB to come up with a more streamlined deposition of TLS information for PHENIX. There are some other issues that need to be resolved first that have slowed this down a little. - I am in agreement with George (not unusual). - As far as I remember Garib was supportive of the idea of no longer depositing residual B-factors in the atomic iso-B column. - What phenix.refine writes in the PDB file is almost exactly the same as you would get by running TLSANL on a REFMAC PDB file. - It is my understanding that the EBI runs TLSANL on REFMAC deposited PDB files to extract the ANISOU records so that R-factors can be calculated. It would seems that this information is then discarded. [I could be mistaken about this whole process though] - Allowing ANISOU records only when atomic anisotropic displacement parameters have been refined seems very restrictive. There may be multiple ways to arrive at anisotropic displacements other than the traditional method (TLS is one, George mentioned TLS restraints instead of constraints, and we have some ideas about ADP refinement that would also result in anisotropic displacements). - It is good to remember that TLS refinement is constrained anisotropic displacement parameter refinement. - If we want bioinformaticians to analyze our structures then we should be writing something in the iso-B column that they can understand - I favour the iso-B equivalent of the total atomic B-factor. This I assume they can handle. I very much doubt that anyone other than a crystallographer will go to the trouble of extracting the TLS information and recalculating atomic displacements. - The biologists looking at structures from the PDB do not care about TLS or ANISOU records. If they choose to look at anything it will be the iso-B column (probably by colouring the atoms by B-factor in a display program). I'd like to give them a fighting chance of seeing something meaningful such as the iso-B equivalent of the total atomic B-factor rather than a residual B-factor (which has no meaning to them). - I will not be holding my breath waiting for any of the popular display programs to start interpreting TLS header information. - I agree that it is best for everyone if we have some clear standards for deposition and tags that make it clear to anyone looking at files from the PDB what is meant by the contents. The PDB is very aware of this and I expect things to be straightened out fairly soon in collaboration with the developers of phenix.refine and REFMAC. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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Rant: B vs TLS, anisou, and PDB headers
by Frank von Delft 30 Mar '08

30 Mar '08

Just spent an hour trawling docs, BBs (recent threads) and logs to figure out what the hell my B column is telling me (phenix vs refmac vs pdb). Oh dear, it's a disaster area, quite Heissenbergian... the most important number (uncertainty) is itself unknowable: * Phenix writes total ADP, Refmac writes residual ADP. * Refmac writes a remark -- pdbdep strips it (!?!!?) * Phenix writes no remark (I think?) * Refmac writes different numbers to TLSOUT and pdb header (trace of S) * Phenix duplicates the information in header (TLS) and ANISOU cards, the latter thereby making implicit what should be explicitly stored: how the ADPs are connected. * Refmac, given phenix TLS-originating ANISOUs, flattens them into first number, but does not remove them * PDB does not care I'd like to appeal for an urgent consensus -- which should be unusually easy, since it involves only two programs and one repository. My strong recommendation, from first principles of usability: residual B into ATOM, no TLS in ANISOU, and the rest into the header. I know it's religious, but here's the reasoning: ==> the end-user looks *locally*, that's what ATOM and ANISOU are for. ==> global stuff (cell, symmetry, NCS, and yes, TLS) belongs in the header -- as do what's still missing, namely twinning, lattice modulations, scatter factors, and restraints. Yes, we crystallographers want easy B-factor stats (phenix's reason), but then lets fix the analysis programs to look at the header as well. And yes, packing and internal motions (TLS) are all very important for analysis - but that is why it should be explicit in the header, so that graphics tools have easy access to it. End rant (but not end hope :) phx.

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error when optimize_wxc w/o optimize_wxu turned on
by C. Briand, Biochemisches Inst. 28 Mar '08

28 Mar '08

Dear Phenix Users, We are currently using the last version of phenix in our lab. ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 2008_02_08_1610 Release tag: rc6 User: briand ------------------------------------------------------------------------------- When we are using phenix.refine to refine a structure and we are turning on optimize_wxc w/o optimize_wxu, the job failed. Any ideas ? Many thanks Christophe =============================================== Dr. Christophe Briand Biochemisches Institut Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland http://www.bioc.uzh.ch/gruetter/ ===============================================

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sugar links
by Alessandro Nascimento 28 Mar '08

28 Mar '08

Hi all, I'm trying to apply a cif link modification for MAN-MAN link and found this post explaining how to do that: http://www.phenix-online.org/pipermail/phenixbb/2007-July/000332.html However the syntax refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } gives me the following error *** apply_cif_link: data_link: NAG-NAG-b-D Sorry: Missing CIF link: data_link_NAG-NAG-b-D Please check for spelling errors or specify the file name with the link as an additional argument. *** Has the syntax changed or am I missing something? thanks a lot in advance, --alessandro phenix.refine --version: ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 2008_02_08_1610 User: Alessandro -------------------------------------------------------------------------------

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large ASU: problem with upper/lower case chain IDs
by Cherepanov, Peter P 26 Mar '08

26 Mar '08

Dear phenix developers, I am new to this list and apologize in advance if the following has been discussed before. Although, I must say, the problem is rather unusual... well, we are trying to refine a structure with 36 protein chains per asu (not much fun, but it is our best crystal form for this protein). The chains are labeled (by phaser) with UPPER and lower case characters. THE TROUBLE IS, phenix.refine confuses upper and lower case chain IDs. Now, although default refinement (no restraint_group definitions) works, it is very important for us to define groups of residues, in particular, for NCS. I tried defining chains using quotes (e.g chain "i"; or chain 'i', or "chain i", etc,etc), which did not help. Phenix chokes on our pdb file also after automatic NCS search (although it finds and defines ncs groups correctly). It is funny, because, the program does discriminate between upper and lower case characters when referring to an element (e.g. it does not accept "element Se" when coordinate file has got "SE" and vice versa). Analogous refinement (and NCS definitions) works great in Refmac; but would like to compare results and also take advantage of simulated annealing in phenix.refine. Is there a quick fix, without tedious relabeling the chains? In principle, we could use upper case characters, followed by digits 0-9 [that works], but this would make the whole process very difficult for a number of reasons; I hope there is way around it, thank you, Peter PS: we are using v1.3b

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ADP high variance
by Daniel Frey 26 Mar '08

26 Mar '08

Hello, I have a good data set to 1.8 A and refined it with the actual version of phenix, including annealing and isotropic bfactors. Checking the B factor variance in coot revealed high differences in about 50% of the residues. Most of them are at the surface, but still there are residues like phenylalanines and valines within the core where the bfactors jump from 25 to 50 from one carbon atom to the other. Changing wu and wxu_scale did not improve the results. A quick check with refmac improved the results, so i guess I am missing the right restraints for phenix. Which parameters should be changed to improve the bfactor variance in phenix? Thanks for your help Daniel Daniel Frey Department of Biochmistry University of Zurich Winterthurerstrass 190 8057 Zurich Switzerland freyd(a)bioc.unizh.ch Tel: +41446355558 www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch

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Scientific Writer Position, Berkeley California
by Paul Adams 24 Mar '08

24 Mar '08

= = ======================================================================== PSI Knowledgebase Scientific Writer, Lawrence Berkeley National Laboratory = = ======================================================================== Scientific Writer/Editor Division: Physical Biosciences SUMMARY: We are seeking an intelligent and motivated structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position will require interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH- funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI-developed technologies to the broader scientific community, and editing a web portal describing these technologies. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. DUTIES: Essential - Primary duties and responsibilities will include regular communication with researchers at the PSI-funded structural genomics centers and other programs. Interaction with other groups in the PSI Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. Collecting information describing technologies from other PSI-funded researchers and by the use of web and bibliographic search tools. Writing text that describes new technologies to the broad scientific community. Maintaining and editing written and graphical material on a web site devoted to technology dissemination. Extensive email and verbal interaction with other researchers. Marginal - Analysis of crystallographic data. QUALIFICATIONS: Essential - BS, MS or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Marginal - Experience with the solution of macromolecular structures using crystallographic or NMR methods. Practical computational analysis of crystallographic data. Familiarity with scripting languages such as Python. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 21575. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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