- phenixbb - phenix-online.org

Searchable phenixbb
by Mark Collins 11 Apr '08

11 Apr '08

Hi phenix community Is there a search function for this bb, as there is for the ccp4bb? I have some questions about twinning, TLS and alternate conformations in phenix.refine. I hate repeating questions that have been answered previously but going thru the Archives month by month is proving to be a little slow. Thanks Mark Collins

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Persistence of CONECT records?
by Warren DeLano 10 Apr '08

10 Apr '08

Though I wouldn't mind PyMOL taking credit for CONECT valence encoding, this was in fact a convention originally employed by MacroModel which I adopted from Schrodinger. According to OpenBabel maintainer Geoff Hutchinson, it is also a convention supported by the OpenBabel chemical interchange software, and it according to OpenEye's docs, OEChem supports it as well (with the OEPDBFlag::ORDERS, BONDS, and BOTH flags to OEWritePDBFile). Given that four popular tools already support this convention, shouldn't PHENIX do so as well? ________________________________ Message: 4 Date: Thu, 10 Apr 2008 12:53:27 -0400 From: "Schubert, Carsten [PRDUS]" <CSCHUBER(a)prdus.jnj.com> Subject: [phenixbb] Persistence of CONNECT records? To: <phenixbb(a)phenix-online.org> Message-ID: <889E20E3723D0C45A493DA5DA87D854E01E876B6(a)JNJUSRAGMS02.na.jnj.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

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Persistence of CONNECT records?
by Schubert, Carsten [PRDUS] 10 Apr '08

10 Apr '08

Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

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Ignoring SegIDs
by Stephen Graham 10 Apr '08

10 Apr '08

Hi all, Apologies if this is a dumb question, but... Is there a way to get phenix.refine to ignore segids? I ask because COOT seems to be blithely unaware of segids and they have a habit of disappearing when one is rebuilding a model, resulting in very odd geometries when the side chain of a residue is in segment ' ' and the main chain is in segment 'A'. Alternatively, is there a 'convert chain IDs to segids' option like in CNS? Basically, I would like the segids removed/fixed/ignored automagically at the start of refinement (since I never use them for anything useful anyway). Thanks, Stephen -- 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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phenix-cns conversion
by Sean Johnson 08 Apr '08

08 Apr '08

What is the best way to convert phases obtained from phenix to a usable cns format? I have 3.6 A maps that were SAD phased and density modified using phenix. I now want to use some of the cns refinement options - like torsion angle refinement. I tried converting structure factors and HL coefficients to cns format using phenix.reflection_file_converter, but when I run cns input files, I start getting errors like the ones shown below (this is from density_modify.inp): _____ Program version= 1.2 File version= 1.2 %XMAPASU-AUTOmem: increasing memory allocation to 2000000 Minimum brick that covers asymmetric unit: A= 0,..., 150 B= 0,..., 150 C= 0,..., 36 Sum of 21042 elements = 21042.0000 SHOW: average of 810150 elements= 0.0000 ANOMalous=FALSe {OFF} XMPST: average = 0.0000 minimum = 0.0000 maximum = 0.0000 XMPST: r.m.s. = 0.0000 norm = 0.0000 XMHISTO: (default from map) RHOMIN and RHOMAX = 0.0000 0.0000 %XMHISTO-ERR: a complete flat map. XMHISTO: (default from map) SLOT width = 0.000000 %XMHISTO-ERR: the SLOT width is too small 0.00000 XMHISTO: the number of slots MBINS=10000 and width SLOT= 0.0000 %XDOTYPE-ERR: Variable/type mismatch: do (masksol=1) (real(automap) <= $cutoff) ^ %DO-ERR: Data type mismatch. Selection must be a logical expression.: do (masksol=1) (real(automap) <= $cutoff) ^ %SHOW error encountered: There were errors in DO expression. (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. ______ I'm guessing that the problem has to do with the way I am converting the data to cns (since I have beautiful maps from phenix), but I'm really stuck right now. Any guidance would be appreciated. Thanks, Sean Johnson -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

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ICSG 2008 Oxford Sept. 20-24, 2008
by Tom Terwilliger 07 Apr '08

07 Apr '08

Dear PHENIX users, I would like to encourage you to attend the 5th International Conference on Structural Genomics Sept 20-24th! This is the principal conference on structural genomics; it occurs every 2 years in a different part of the world. This year's meeting is in Oxford, UK and will have a lot of methods talks in addition to structural biology results. You can register at http://www.spine2.eu/ISGO . I'll look forward to seeing you in Oxford in September! All the best, Tom T The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. The Scientific Program will contain main scientific sessions, poster sessions, breakout discussion groups for specific topics and a social program and we expect to attract a worldwide audience of 500 delegates. Provisional Session Topics - Structural genomics, systems biology and complexes - The impact of structural genomics on treating diseases - Maximising impact on and integration with biology - HTP methods for membrane proteins - Hybrid/multidisciplinary approaches - Strategies for intrinsically unfolded proteins - Should we expand the protein universe or concentrate on biology? - New technologies The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration and abstract submission is now available. Early registration and abstract submission deadline: 31st July 2008 http://www.spine2.eu/ISGO Social program reservations closing date: August 31st 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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"unlimit" command with Phenix GUI -unlimit: descriptors: Can't remove limit (Invalid argument)
by hari jayaram 03 Apr '08

03 Apr '08

Hi I am giving new to Phenix and the Phenix GUI. For starters I am trying to run the prime and switch strategy in Phenix. I know all my inputs are fine (see below) but the program aborts ( GUI turns red ) after a few seconds. I checked the resolve.com file in the directory and it has a command "unlimit" which in Leopard causes the following output to be echoed to the stdout "unlimit: descriptors: Can't remove limit (Invalid argument)" Once I deleted the unlimit command I can run the script just fine from a shell. My question is how can I tweak the Phenix GUI so that I dont have to run everything from the shell by manually editing the resolve.com file. The script that stops the GUI is reproduced here. Thanks for your help Hari Jayaram Postdoc , Brandeis University script: #!/bin/csh setenv SOLVEDIR /usr/local/phenix-1.3b-rc6/solve_resolve/ext_ref_files setenv SOLVEBIN /usr/local/phenix-1.3b-rc6/build/mac-intel-osx/solve_resolve/exe # setenv CCP4_OPEN UNKNOWN setenv SYMOP $SOLVEDIR/symop.lib unlimit # $SOLVEBIN/resolve<<EOF access_file mirima.dat labin FP=F_s3-3 FC=FC PHIC=PHIC FOM=FOM FWT=FWT hklin resolve_input.mtz mask_cycles 5 minor_cycles 10 hklout testpms-resolve.mtz no_build prime_and_switch EOF unlimit returns------------> [mango:hj/s3-3/prime_switch] hari% unlimit unlimit: descriptors: Can't remove limit (Invalid argument)

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Crystallographic Postdoctoral Research Position - Berkeley, USA
by Paul Adams 01 Apr '08

01 Apr '08

A postdoctoral research position is available immediately to work on challenging problems in structural biology: Postdoctoral Researcher Job ID: 21615 Division: Physical Biosciences Date Opened: 3/28/2008 This postdoctoral position will study the structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position will be joint between the Center for Protein Folding Machinery (proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). The biological systems to be studied will include: Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells, Glycosyl transferases responsible for the synthesis of hemicellulose in plants, and Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. The candidate will have experience with using crystallographic methods to study macromolecules; robotic hardware for performing crystallization trials and imaging trays are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. Essential: Primary duties and responsibilities will include using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Marginal: Use of small angle X-ray scattering methods to analyze macromolecular complexes in solution. Essential: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Marginal: Experience with the use of small angle scattering methods. Familiarity with robotic hardware for crystal growth. 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. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the Center for Protein Folding Machinery visit: http://proteinfoldingcenter.org/ and the Joint BioEnergy Institute visit: http://www.jbei.org/. For more information about the Berkeley Center for Structural Biology visit: http://bcsb.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 21615. 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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TLS, B factors, phenix and refmac
by Mischa Machius 01 Apr '08

01 Apr '08

Hi - Prompted by the recent discussions on B values, TLS refinement and differences between Phenix and refmac, we looked into these matters in more detail. We found that the crux of the problem lies in the fact that TLS and B value refinements are usually decoupled. We have developed a formalism that rolls both TLS and B value refinement into one. Phenix and refmac were modified to carry out the calculations, and the outputs from both programs were made compatible to allow proper comparison of the results. We found that the stability of the refinements is now vastly improved. More importantly, however, due to the reduced number of parameters, these calculations can be carried out to resolutions of 7 Å with meaningful representations of indiviual, anisotropic atomic displacement parameters. This low-resolution limit required reformulating the calculation of Wilson B values, but that is only a minor aspect of our treatment that can be neglected. The new, combined procedure for the simultaneous refinement of TLS/B is called 'TBS' refinement, reflecting all required components: Translation, Bibation, Screw. Interestingly, the ‘T’ component is fairly insensitive to input parameters, whereas the overall quality of the refinement is greatly dependent on the ‘B’ component. The more emphasis is put on ‘B’, the more convincing the results. There is a limit, though. At very high levels of ‘B’, the so-called ‘bibacity limit’, the refinement becomes very unstable, leading to inversion in severe cases. Seasoned crystallographers familiar with the concepts can successfully push the procedure to quite high 'B limits', whereas less experienced practitioners should follow the protocols very carefully. Please contact us for any details. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

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Question about anisotropic refinement of selected waters during automatic solvent update
by Schubert, Carsten [PRDUS] 01 Apr '08

01 Apr '08

Hi, I am trying to refine a couple of waters in a structure anisotropically in the latest version of CCI-Apps (Feb-08) . The selection is: refine.adp.anisotropic = "chain W and (resid 25 or resid 54)" The refinement works fine if "main.ordered_solvent = False". When I enable "main.ordered_solvent" the refinement fails with: "Sorry: Bad (empty or mixed) selection in adp_individual.aniso" during the first update of the solvent in macrocycle 1. A workaround is easy to implement, but I think this kind of scheme should work. Although it has all kinds of tricky implication for the downstream handling of the selection if the residues/waters in questions are deleted.... Cheers, Carsten

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gnomebreakpad error
by shivesh kumar 01 Apr '08

01 Apr '08

Dear all, We are trying to install phenix in Fedora Core 8.While installing it is showing the following error- Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory Please suggest what is wrong or missing. Thanx in advance. Shivesh

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tls definitions
by PhilEvans 01 Apr '08

01 Apr '08

Sorry if this has been answered before, but I've only just joined this BB In phenix.refine, I'm trying to make TLS groups consisting of multiple chains, eg refinement.refine { strategy=individual_sites+tls+individual_adp adp { tls="chain A and chain B and chain Z" tls="chain C and chain D and chain Y" } } but it doesn't work: what should I do? Phil ================== Extract refinement strategy and selections ================= individual_sites = True rigid_body = False individual_adp = True group_adp = False tls = True individual_occupancies = False group_occupancies = False group_anomalous = False size = 1356 n_use = 1356 n_use_u_iso = 1356 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 1356 Sorry: Empty selection in adp_tls selection.

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question about refinement in a SAD data set
by Pascal EGEA 30 Mar '08

30 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 29 Mar '08

29 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 29 Mar '08

29 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 27 Mar '08

27 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 25 Mar '08

25 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 23 Mar '08

23 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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Beamline Scientist Position, Berkeley California
by Paul Adams 23 Mar '08

23 Mar '08

= = = = = = = ======================================================================== Beamline Biophysicist Scientist/Engineer, Lawrence Berkeley National Laboratory = = = = = = = ======================================================================== Biophysicist Scientist/Engineer Division: Physical Biosciences SUMMARY: As a member of the Berkeley Center for Structural Biology (BCSB), provide technical and scientific support for users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California. Work with the BCSB group leader and other BCSB scientists and engineers to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation. Participate on projects involving the structure determination of biological molecules and biomolecular complexes. 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 - Provide support for users regarding data collection, processing, archiving, and analysis. Play a role in coordinating and participating in engineering projects to advance the capabilities of the beamlines, with a focus on robotics systems for sample handling. Participate in the development of instrumentation and methodology for biological crystallography. Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. Required to occasionally work off-hours and weekends to support users. Marginal - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. QUALIFICATIONS: Essential - Substantial experience working in the area of synchrotron science using complex instrumentation and computer controls. Experience with robotics hardware and control systems. Experience with the collection of experimental data for biological crystallography. Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. Experience in the use of computer programs required for biological crystallography. Ability to work in a team environment and effectively interact with a broad range of colleagues. Marginal – M.S. or Ph.D. in physics, biology, bioengineering, biophysics, or related field. Experience in UNIX computing. To apply: visit http://cjo.lbl.gov/ and search for the keyword BCSB or the job number 21576. 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. --

1 0

Perfect Twins and Ligand Fit or AutoBuild
by Mary Fitzgerald 20 Mar '08

20 Mar '08

I've got a perfect merohedral twin that is refining quite nicely using phenix.refine. In my detwinned FoFc maps, I see density for for a previously diordered region of protein and at least one ligand I soaked in, possibly more. If possible, I'd like to automate the placement of the ligand and build of the diordered region. The data is 3A so it might not work all that well. From looking at LigandFit( I haven't taken a close look at Autobuild yet), I don't see a way to tell the wizard I have twinning. So, can I use Ligand Fit or Autobuild with twinned data? Will the wizards work if I feed it detwinned data and is there a way to get phenix.refine to output the detwinned data other then as map coefficients? Another question/comment. Can I make detwinned 3Fo-2Fc maps? When I tried using the February version of cci_apps, I got an error when I changed the coefficients on my maps in my phenix.def file. Thanks, Mary

3 2

How to use the STIR command in phenix.refine?
by nick＠silvaggi.com 13 Mar '08

13 Mar '08

Hello, I am refining a high-resolution X-ray structure and I would like to gradually increase the resolution from 1.5 to 1.0A, as I used to do in shelxl. I know the STIR command is the way to do this, but I cannot figure out the syntax to use. Currently I am using the following commands: high_resolution = 1.0 low_resolution = None stir = 1.5 When I run phenix.refine (2008_02_08_1610) it echos a line that says "STIR 1.5" before the first macrocycle, but at each stage I see "(resolution: 1.00 - 21.77)." Obviously I am not using the STIR command correctly. Any advice would be greatly appreciated. Thanks in advance. Nick Silvaggi Department of Physiology and Biophysics Boston University School of Medicine 715 Albany St. R-702 Boston, MA 02118

2 1

Beam Time at BCSB beamlines in Berkeley
by Peter Zwart 13 Mar '08

13 Mar '08

============================================================= Synchrotron Beam Time available for Macromolecular Crystallography at Berkeley Center for Structural Biology Beamlines (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2). The ALS is now accepting General User applications for May/June ============================================================= The Berkeley Center for Structural Biology (BCSB) operates five beamlines at the Advanced Light Source in Berkeley. Beamlines 5.0.1, 5.0.2 and 5.0.3 are equipped with the Berkeley Automounter system. Beamline 8.2.2. has a Rigaku Actor sample mounter capable of handling Rigaku, unipucks and ALS style pucks. Beamlines 5.0.2, 5.0.3, 8.2.1 and 8.2.2 have large 3x3 Q315 or Q315r CCD detectors. Beamlines 5.0.2, 8.2.1 and 8.2.2. are MAD stations, whereas 5.0.3 and 5.0.1 are fixed energy beamlines at the Se high energy remote, suitable for Se-SAD experiments. The beamlines generate between 1.5x10^11 and 8x10^11 photons per second of flux into a 100 micron collimator at 1.5 mrad divergence. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for beamtime at these, or any other ALS macromolecular crystallography beamlines, please submit a General User proposal by March 15, 2008 in order to be considered for the May-June schedules. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize You can also request access to any open beam time on the five BCSB beamlines by e-mailing our scheduler at SLOrtega(a)lbl.gov. Any industrial or academic group interested in becoming part of the Participating Research Team for beamlines 5.0.1 and 5.0.2 should contact the Head of the BCSB (Paul Adams: PDAdams(a)lbl.gov, 510-486-4225). (Please note that executed user agreements and proprietary fees, if applicable, must be received at least five working days prior to scheduled beam time.) -- Peter Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron road, Berkeley, CA-94720 Cell: +1 510 289 9246 Fax: +1 510 486 5664

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Collaborative Crystallography
by Banumathi Sankaran 11 Mar '08

11 Mar '08

The Berkeley Center for Structural Biology (BCSB) is pleased to announce a new Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists are able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program provides a number of benefits to researchers: * Obtain high quality data and analysis through collaboration with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. CC proposals go through the regular ALS General User proposal review process. They are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the projects to fit into the available resources. Please note that only non-proprietary projects are currently being accepted. In keeping with similar programs the BCSB staff researchers who participate in data collection and/or analysis should be appropriately acknowledged as authors on publications and/or PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography How To Apply: To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for Mai/June, 2008, proposals must be submitted by March 15, 2007. Questions: For comments or questions, feel free to contact Banumathi Sankaran (BSankaran(a)lbl.gov) or Gari Kloss (MKloss(a)lbl.gov)

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refine error when optimize_wxc w/o optimize_wxu turned on
by shi jiahai 11 Mar '08

11 Mar '08

Hi, Dear all, I was using phenix.refine to refine the structure. Once I turned on optimize_wxc w/o optimize_wxu, the job failed with the following message. ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc The phenix I used is the latest version, 1.3b rc6. The platform is intel-linux-2.6 redhat-e4. Python is 2.4.2 Could anyone please tell me what the problem is? Thank you very much! -- Best Regards, Shi Jiahai

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autobuild errro message
by Christine Gee 05 Mar '08

05 Mar '08

Hi I was using phenix.autoMR and when it tried to go on to autobuild the job ended with the following error message AutoBuild Input failed can only concatenate list (not "str") to list There are two molecules in the asymmetric unit. I tried running phenix.autobuild with the output pdb from molecular replacement and got the same message. The file looks OK to me though. Can you tell me what the problem is? Regards Christine

2 1

problem compiling phenix 1.3 beta rc3
by Melody Lin 05 Mar '08

05 Mar '08

Dear all, I have a problem compiling phenix-1.3beta-rc3 on my Mac OSX tiger ppc. I downloaded the tar file under the sbgrid directory and issued command "sudo ./install" to compile it after unzipping. Everything went OK until the last step when the installer is trying to compile phenix components, ands says it will take an hour, but in 2 minutes it reports failure for the compilation. Could anyone suggest what problem this is? Did I download the wrong tar file? Your input is greatly appreciated! Best, Yan

5 6

Question about occupancy refinement of riding hydrogens
by Schubert, Carsten [PRDUS] 04 Mar '08

04 Mar '08

I just noticed that occupancies of riding hydrogens are being refined by default, in fact I am unable to turn this feature off (CCI-APPs from Jan-8). I was just (very naively) wondering what is the rationale behind this? The B-factor refinement for riding hydrogens is already enabled and should take care of this or not? It looks a bit odd to have hydrogens with occupancy 0.9 sitting on a carbon with occupancy 1.0 at 2.0 A resolution. Cheers Carsten

2 1

Enhancement request for map formats
by Schubert, Carsten [PRDUS] 04 Mar '08

04 Mar '08

Hi, I was wondering if it would be possible to have the choice of generating ccp4 maps in phenix.refine. This type seems to be best compromise so far between compatibility and size. The xplor type ascii maps are 10x the size and do not offer any advantage in a homogeneous OS environment. Converting the maps after the fact is one more step I am trying to eliminate. Cheers Carsten

2 4

Possible to rebuild only certain residues in a molecule?
by Francis E Reyes 03 Mar '08

03 Mar '08

All Can the rebuild process be directed to rebuilding specific residues in the molecule? Can this be extended to build multiple models of a given set of residues? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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problem with a twinned data set
by Pascal EGEA 02 Mar '08

02 Mar '08

Hi All This a question of general Crystallography and use of Phenix to deal with twinned data. I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong? Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output. ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.36 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law 0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found --------------------------------------------- Analysing possible twin law : -l,k,h --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115 Britton analyses Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955 By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit. Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1) I will greatly appreciate your input, many thanks. Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

4 4

ligand refinement - elbow
by Christine Gee 01 Mar '08

01 Mar '08

Hi Its taken me a while to get around to it, but I just ran elbow to create a cif file etc for my inhibitor, but the bond lengths are quite different from what I got from the PRODRUG server, and it seems that the pdb file I got out of elbow has a few problems (COOT doesn't join up the aromatic ring for example because the carbons are now too far away on one part of the ring). I was wondering how the bond lengths are selected? It seems it is giving the aromatic carbons a bond length of 1.5, when my previous file (and phenylalanine for example have 1.3). Also, I still am not 100% sure how to add the CONNECT information to make the ligand able to covalently bind to the protein. Regards Christine

3 2

refinement problems
by Christine Gee 29 Feb '08

29 Feb '08

Hi This is a more general crystallography question maybe. I am using phenix.refine and I have a model structure refined against data at 3.4A. The model was built from experimental phasing. I reprocessed the same dataset, to include another angstrom resolution (3.3). It has 50% of the data from 3.4 to 3.3 and the I/sigI is about 2. When I refine my structure at 3.4 the stats are 32 and 36 for R and Rfree, but when I use the phase extended data (and the same reflections are the test set up to 3.4A as long as CCP4i did the job right with setting the Rfree) the stats suddenly jump to 49 and 56 when I refine the model against the higher resolution data. Is there something I am missing? I am doing a rigid and an anneal before individual sites and adp refinement. The space group is P3121. Regards Christine

2 1

input initial TLS parameters
by iulek 24 Feb '08

24 Feb '08

Dear all, I tried to find a way to input initial TLS parameters for the groups into phenix. I know many times this is not advisable, but I wanted to test what comes out from TLSmd server. I could not find any reference on how to do this. Note that I know how to define the groups (a previous question in this bb), the point now is to input initial parameters (origin, T, L, S). Thanks, Jorge

5 7

ligand refinement
by Christine Gee 22 Feb '08

22 Feb '08

Dear Phenix developers I have a covalently bound ligand in my structure and I would like to use phenix to refine the structure. The ligand is bound to the sulfur of a cysteine. What is the best method for defining the ligand. Should I generate a cif file for the whole amino acid and the ligand, or can I make one for just the ligand and add in some restraint somewhere which tells phenix to make a bond between the ligand atom and a nearby sulfur in a cysteine. If I generate a cif file with the whole amino acid and ligand, I assume I will I have to follow some convention in atom naming so that the main chain bonds and angles will form and refine OK? Regards Christine

3 2

Phenix.refine Questions
by Mary Fitzgerald 22 Feb '08

22 Feb '08

First, I have a hopefully easy question. I can't seem to figure it out although feel like I should be able to. Is there a way to run a phenix.refine job in the background? I tried using the & like I usually do and it didn't work. It would be nice to start a job and go home without leaving myself logged into the computer. I didn't see anything in the documentation which makes me think I'm being dull. Second, a technical question. When phenix.refine does ordered solvent, does it use detwinned maps if you've put in the appropriate twin operator and indicated it was twinned? When I've tried running phenix.refine with my perfect twin, it doesn't seem to find waters like I can using the CNS twinned water picking script. Third, is it possible to run phenix.refine in parallel at all. My structure is annoying large and the parallelization of FFT in CNS seems to help speed things up abit. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

4 4

geometry in phenix.refine
by Jianghai Zhu 21 Feb '08

21 Feb '08

Hi, I recently noticed that the geometry in my structure is much worse than my previous model. Here are some examples. The RMSD results after a refinement by phenix 1.3b. stage angl bond chir dihe plan repu 3_bss: 0.711 0.009 0.059 18.282 0.002 3.917 after switching to cci version 2008_02_08_1610, I tried to do a geometry minimization by setting wxc_scale = 0. The RMSD I got from the previous model is as following. stage angl bond chir dihe plan repu 0 : 1.394 0.124 0.147 20.782 0.004 3.925 and after 6 macro cycles of geometry minimization, stage angl bond chir dihe plan repu 6_bss: 0.622 0.011 0.120 13.143 0.003 3.822 It funny that the RMSD are so different for the same model. What happened? Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D Immune Disease Institute Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Re: [phenixbb] Phenix.refine Questions - specifically running Phenix in the background
by Edward Snell 21 Feb '08

21 Feb '08

Re: <quote> Message: 8 Date: Thu, 21 Feb 2008 14:23:24 -0500 From: "Mary Fitzgerald" <mary.x.fitzgerald(a)gmail.com> Subject: [phenixbb] Phenix.refine Questions To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Message-ID: <2fc50e280802211123h192c095x9c65f5bd6f1d4a55(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" First, I have a hopefully easy question. I can't seem to figure it out although feel like I should be able to. Is there a way to run a phenix.refine job in the background? I tried using the & like I usually do and it didn't work. It would be nice to start a job and go home without leaving myself logged into the computer. I didn't see anything in the documentation which makes me think I'm being dull. </quote> Apologies if someone has already answered this but you can set up a little command file e.g. 'refine.com', something along the lines of: phenix.refine model_from_coot.pdb data.mtz ligand.cif my_favourite.params --quiet With all your parameters in 'my_favourite.params' and run it with > nohup ./refine.com & You can then log off and check it later and it will still be running. The key seems to be the nohup and the '--quiet' switch. Works for me, hope it works for you. Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: esnell(a)hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!

1 0

refining nucleic acids, formats?
by Green, Todd 20 Feb '08

20 Feb '08

Hello All- I'm trying to refine some RNA and I can't seem to get phenix to read in my pdb file as it seems to not recognize the the nucleic acid as nucleic acid, as opposed to protein. By comparison to another pdb from the rcsb site(3b31) I seem to be following the same convention. Any suggestions on what I am doing wrong? I do have protein in the pdb as well. The protein has a different chain id. I am running phenix-1.24.1b, my next move if I can't figure this out is to upgrade. Do I have the format of the RNA wrong? Here is the error message and below that is an example of the first residue of the rna. Cheers- Todd *********************************** sorry the PDB file xxx.pdb has an incomplete residue (or conformer/residue combination) in conformer '' chain R residue U 1 because this conformer is missing the following main-chain atoms: ['N', 'CA', 'C'] *********************************** ATOM 18243 O5' U R 1 50.409 12.832 14.548 1.00144.33 O ATOM 18244 C5' U R 1 49.763 12.566 15.794 1.00144.88 C ATOM 18245 C4' U R 1 49.745 13.804 16.678 1.00145.19 C ATOM 18246 O4' U R 1 49.036 13.579 17.920 1.00145.17 O ATOM 18247 C1' U R 1 49.400 14.624 18.811 1.00145.36 C ATOM 18248 N1 U R 1 49.443 14.148 20.242 1.00145.47 N ATOM 18249 C2 U R 1 48.886 14.949 21.229 1.00145.51 C ATOM 18250 O2 U R 1 48.347 16.024 21.005 1.00145.55 O ATOM 18251 N3 U R 1 48.976 14.439 22.507 1.00145.32 N ATOM 18252 C4 U R 1 49.555 13.242 22.895 1.00145.27 C ATOM 18253 O4 U R 1 49.558 12.920 24.081 1.00145.43 O ATOM 18254 C5 U R 1 50.118 12.468 21.816 1.00145.29 C ATOM 18255 C6 U R 1 50.045 12.940 20.562 1.00145.32 C ATOM 18256 C2' U R 1 50.735 15.197 18.331 1.00145.42 C ATOM 18257 O2' U R 1 50.561 16.545 17.935 1.00145.28 O ATOM 18258 C3' U R 1 51.102 14.243 17.192 1.00145.51 C ATOM 18259 O3' U R 1 51.827 14.863 16.146 1.00146.05 O

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workshop abstract
by Tom Terwilliger 19 Feb '08

19 Feb '08

Hi Peter he is an abstract for my talk. Thanks! -Tom T Phenix Wizards -- Automation of the Structure Determination Process The PHENIX Wizards allow automation of major steps in the structure determination process. The Wizards carry out decision-making, provide suggestions for the user, and form a flexible environment for investigating alternative strategies for structure determination. New algorithms available in PHENIX include a Iterative-build OMIT procedure for prevention of model bias and ligand identification in electron density maps. The PHENIX AutoBuild Wizard can carry out iterative model-building, density modification and refinement to improve the quality of models at resolutions as low as 3 Å. Electron density maps calculated using an atomic model can be affected by model bias introduced during refinement of the model. We have developed a Iterative-build OMIT procedure that prevents model bias in iterative procedures for model-building and refinement while producing a high-quality electron-density map. The PHENIX LigandFit automated ligand-fitting Wizard can fit flexible ligands into an electron density map. The Wizard can identify unknown ligands by comparing a set of potential ligands to the map and finding the one that fits the density most closely. 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

1 0

Re: [phenixbb] Clashes problem
by Pavel Afonine 13 Feb '08

13 Feb '08

Hi All, 1) phenix.refine has a standard set of geometry restrains as other refinement programs: bond, angle, planarity, chirality, dihedral, non-bonded. Clash score is not something that is included into refinement as a target and then used directly in refinement. Clash scores may be bad at the beginning of structure refinement and should be good at the end. 2) Using H atoms as a riding model should normally help in fixing clashes, however it's not 100% guaranteed: some clashes may be "locked" so the refinement cannot overcome the barriers even with H atoms. In this case what's Luca Jovine suggesting (see one of the emails in this thread) is an excellent thing to do (to add to his receipt: you may also consider using more than default number of macro-cycles). Running simulated annealing is also helpful (use "simulated_annealing=true" flag for this). 3) Since handling of H atoms in phenix.refine is significantly improved in newer versions, I would warmly recommend to use the latest phenix.refine available (currently from CCI Apps: http://www.phenix-online.org/download/cci_apps/). 4) Also, clashes related concerns may be a result of inoptimal weight between Xray target and restrains. Although one can play with the weight adjusting scales manually by trying different values of "wxc_scale" parameter ("wxu_scale" is analog for b-factors refinement) the new version of phenix.refine has an automatic procedure for finding the best weight (here "the best" means the weight that leads to the lowest Rfree) (Carsten's suggestion). To use this option: % phenix.refine model.pdb data.mtz your_parameters.par optimize_wxc=true Note this this may take a while to run (depending on resolution and structure size) so consider running it overnight. If none of the above helps, I would be *very* interested to look at the data and model myself to 1) help you find the best strategy to overcome this problem, and 2) find and fix problem in phenix.refine (if any). As always, I promise to keep all data confidential. Pavel.

4 5

alternative conformations
by Dr. Colin W. Levy 13 Feb '08

13 Feb '08

Hi, What is the correct procedure in phenix for dealing with alternative conformations of side chains? Thanks Colin

3 2

Clashes problem
by Simon Kolstoe 11 Feb '08

11 Feb '08

Dear Phenix community, I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A structure (with individual_sites, group_adp, TLS & NCS, wxc_scale=0.1). After refinement I am running the pdb file through the Molprobity server. Molprobity gives a clash score of 33.78 indicating the number of steric clashes (within 0.4A) per 1000 atoms. I am slightly concerned that a refinement program seems happy to allow such clashes. Is this a problem with the version of phenix.refine I am running, or is there a more obvious explanation that I have missed? Thanks, Simon

7 7

Making GDP (non-polymer) into an RNA monomer
by Francis E Reyes 08 Feb '08

08 Feb '08

All I need to attach a 5' modification, a diphosphate guanosine to my RNA. I figure GDP (from the monomer library) has everything I need. However, what needs to be done to make a connection with the next nucleotide in the chain (in both phenix.refine and coot) ? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Re: [phenixbb] Making GDP (non-polymer) into an RNA monomer
by Ralf W. Grosse-Kunstleve 08 Feb '08

08 Feb '08

Hi Francis, > However, what's the etiquette for how the residue should be named in > the PDB? I have it right now as GDP, though Gr seems much more > sensible? Or should I name it something completely custom? If the monomer library GDP matches what you have in the PDB I'd stick with the name. I'd rename the residue only if modifications are necessary. Gr would be a problematic alternative because the monomer library uses that already for RNA Guanosine (mon_lib/g/GR.cif). Ralf

1 0

Re: [phenixbb] lower case chain IDs
by Engin Ozkan 08 Feb '08

08 Feb '08

Thanks, Ralf. We will have the latest CCI Apps installed in our upcoming February software update (which should include your December update), and give it another try. That will probably fix it. Engin Quoting "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov>: > Hi Engin, > >> which, I guess, is the CCI Apps version from August 2007. > > Yes, that explains it. Sorry, when I saw your first message > I should have thought of this immediately. > > To resolve your problem, you'll need the latest CCI Apps. > Multiple CCI Apps versions can co-exist and the installation > takes only seconds. Could you try that? > > http://www.phenix-online.org/download/cci_apps/ > > You can install it under your home directory, i.e. you don't need > special privilleges. > Just make sure you source the setpaths of the version you want to use. > > Ralf >

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lower case chain IDs
by Engin Ozkan 07 Feb '08

07 Feb '08

Hi everyone, We have a case with 32 molecules/asu, and have been using lower-case chain IDs. But we could not figure out how to describe lower-case chain IDs for NCS purposes? In CNS, quotation marks around the segID in ncs.def does it, but that trick does not seem to work in phenix.refine. Thanks, Engin

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A few questions
by Rife, Christopher L 07 Feb '08

07 Feb '08

Hi, We are working on a refinement at 1.14A which was suffering from lots of NPD atoms when refined anisotropically with refmac5 and/or shelx. We followed the guidelines recently posted to this BB, and initially the results looked pretty good, but upon close inspection we have a few questions. We are using Version: 2008_01_09_2058. 1. In our model we have a few solvent ligands, and these show up in the log file as: Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1} Classifications: {'undetermined': 13, 'water': 437} We've used a cif file for EDO with H's when needed, but still see this message. Is this normal? What is unusual? 2. When choosing "indivdual_occupancies" for the refinement, all the atoms within an alt-conf are refined to different occupancies- is this expected? It seems that all atoms in the A conf should have the same value, and the occ of all atoms in the B conf should also be the same. Instead, we see this: ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C ATOM 233 CB AGLU A 28 24.851 7.269 3.672 0.80 9.27 C ATOM 234 CG AGLU A 28 24.978 6.767 2.259 0.66 12.91 C ATOM 235 CD AGLU A 28 23.662 6.717 1.554 1.00 16.51 C ATOM 236 OE1AGLU A 28 22.874 7.667 1.757 0.71 18.78 O ATOM 237 OE2AGLU A 28 23.429 5.733 0.803 0.60 16.77 O ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C ATOM 241 CB BGLU A 28 24.794 7.230 3.713 0.20 6.48 C ATOM 242 CG BGLU A 28 24.877 6.766 2.280 0.34 6.55 C ATOM 243 CD BGLU A 28 23.536 6.702 1.598 0.00 7.53 C ATOM 244 OE1BGLU A 28 23.497 7.014 0.381 0.29 7.85 O ATOM 245 OE2BGLU A 28 22.543 6.341 2.280 0.40 8.40 O 3. Adding hydrogens during anisotropic refinement results in the Parvati server giving "Illegal Biso" errors for many of the hydrogens. I can make the files available if that will help. Thanks, Chris ----------------------------------------- Structure Determination Core Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory

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