- phenixbb - phenix-online.org

Defining an Intermolecular link
by Ryan Timothy Vanderlinden 19 Jan '11

19 Jan '11

Hi, I am working on a complex of three molecules in which, I believe, there is a covalent bond between the sulfur atom of a cysteine on molecule "A" and the c-terminal carbon of molecule "C". There are other structures deposited that have a similar linkage. I have looked at these structures and included a replica description of the supposed link in my input pdb file for refinement. I have redefined this c-terminal residue as a ligand and used phenix elbow do create a .cif file for it. Even when I use the modified pdb file that describes the linkage and the cif file that describes the ligand, the intermolecular link falls apart and the ligand (c-terminal amino acid) separates from the rest of the chain. The resulting mtz file still shows density (2Fo-Fc) supporting the link but the ligand is not in the density. The fact that the ligand moves away from where I would expect it is evidence that modeling the intermolecular linkage is really incorrect or I have not included all the proper files to define this linkage and hold it together during refinement. What are all the necessary files required hold an intermolecular linkage of this nature together during refinement? Are there certain commands that I might be leaving out from my refine script that are necessary to recognize such linkages? Thanks in advance, Ryan VanderLinden University of Utah

3 2

labelit documentation
by Bryan Lepore 19 Jan '11

19 Jan '11

in 1.7-629 (not the latest ), I cannot find any labelit documentation (however, i found some on the labelit site OK). could anyone comment on that - e.g. is there a timeframe, etc. thanks, -Bryan p.s: the interesting CCN article compelled me to look.

2 1

Autobuild: problems with modified amino acids
by Kendall Nettles 19 Jan '11

19 Jan '11

I'm running autobuild from a molecular replacement solution and having two problems: 1. methionines are converted to MSE 2. I'd like to include a .cif file for b-mercapto-ethanol adducted cysteines: CME. The .cif file is one that works for phenix.refine (listed below). I suspect I am not writing the .eff file correctly: refinement.pdb_interpretation.apply_cif_modification { data_mod = cme residue_selection = chain A and resid 530 residue_selection = chain B and resid 381 } Thanks! Kendall Nettles # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.6-289 (Mon Jan 21 12:43:00 2010) # - file written: Sat May 22 10:41:08 2010 # # Input file: /AutoBuild_run_1_/TEMP0/LIGANDS.pdb # Residue: CME # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CME CME 'Unknown ' ligand 21 10 . # data_comp_CME # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge CME N N NH2 . CME C C C1 . CME O O O . CME CA C CH1 . CME CB C CH2 . CME SG S S2 . CME SD S S2 . CME CE C CH2 . CME CZ C CH2 . CME OH O OH1 . CME H H HNH2 . CME H2 H HNH2 . CME HC1 H H . CME HA H HCH1 . CME HB2 H HCH2 . CME HB3 H HCH2 . CME HE2 H HCH2 . CME HE3 H HCH2 . CME HZ2 H HCH2 . CME HZ3 H HCH2 . CME HH1 H HOH1 . # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd CME N CA single 1.450 0.02 CME C O double 1.224 0.02 CME C CA single 1.492 0.02 CME CA CB single 1.497 0.02 CME CB SG single 1.780 0.02 CME SG SD single 2.018 0.02 CME SD CE single 1.783 0.02 CME CE CZ single 1.485 0.02 CME CZ OH single 1.374 0.02 CME H N single 0.913 0.02 CME H2 N single 0.914 0.02 CME HC1 C single 0.965 0.02 CME HA CA single 0.975 0.02 CME HB2 CB single 0.966 0.02 CME HB3 CB single 0.973 0.02 CME HE2 CE single 0.972 0.02 CME HE3 CE single 0.973 0.02 CME HZ2 CZ single 0.976 0.02 CME HZ3 CZ single 0.968 0.02 CME HH1 OH single 0.880 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd CME C CA N 109.05 3.0 CME CB CA N 110.14 3.0 CME CB CA C 110.73 3.0 CME CA C O 119.98 3.0 CME SG CB CA 117.67 3.0 CME SD SG CB 109.52 3.0 CME CE SD SG 109.45 3.0 CME CZ CE SD 117.64 3.0 CME OH CZ CE 117.63 3.0 CME HA CA N 109.56 3.0 CME HA CA C 109.15 3.0 CME HC1 C O 120.00 3.0 CME H N CA 109.48 3.0 CME H2 N CA 109.47 3.0 CME HC1 C CA 120.00 3.0 CME HB2 CB CA 107.69 3.0 CME HB3 CB CA 107.72 3.0 CME HA CA CB 108.19 3.0 CME HB2 CB SG 107.73 3.0 CME HB3 CB SG 107.72 3.0 CME HE2 CE SD 107.78 3.0 CME HE3 CE SD 107.74 3.0 CME HZ2 CZ CE 107.71 3.0 CME HZ3 CZ CE 107.80 3.0 CME HE2 CE CZ 107.71 3.0 CME HE3 CE CZ 107.70 3.0 CME HH1 OH CZ 109.49 3.0 CME HZ2 CZ OH 107.74 3.0 CME HZ3 CZ OH 107.69 3.0 CME H2 N H 109.47 3.0 CME HB3 CB HB2 107.97 3.0 CME HE3 CE HE2 107.93 3.0 CME HZ3 CZ HZ2 107.94 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period CME Var_01 O C CA N 133.07 30.0 2 CME Var_02 SG CB CA N 179.49 30.0 3 CME Var_03 SG CB CA C 58.80 30.0 3 CME Var_04 CB CA C O -105.59 30.0 3 CME Var_05 SD SG CB CA 161.56 30.0 3 CME Var_06 CE SD SG CB -172.66 30.0 3 CME Var_07 CZ CE SD SG 177.33 30.0 3 CME Var_08 OH CZ CE SD 45.37 30.0 3 CME Var_09 HC1 C CA N -45.35 30.0 2 CME Var_10 HB2 CB CA N -58.63 30.0 3 CME Var_11 HB3 CB CA N 57.60 30.0 3 CME Var_12 H N CA C -165.67 30.0 3 CME Var_13 H2 N CA C -45.66 30.0 3 CME Var_14 HB2 CB CA C -179.32 30.0 3 CME Var_15 HB3 CB CA C -63.09 30.0 3 CME Var_16 HA CA C O 13.41 30.0 3 CME Var_17 H N CA CB 72.63 30.0 3 CME Var_18 H2 N CA CB -167.36 30.0 3 CME Var_19 HC1 C CA CB 75.99 30.0 2 CME Var_20 HA CA CB SG -60.78 30.0 2 CME Var_21 HE2 CE SD SG 55.43 30.0 3 CME Var_22 HE3 CE SD SG -60.81 30.0 3 CME Var_23 HB2 CB SG SD 39.69 30.0 1 CME Var_24 HB3 CB SG SD -76.55 30.0 1 CME Var_25 HZ2 CZ CE SD 167.25 30.0 3 CME Var_26 HZ3 CZ CE SD -76.51 30.0 3 CME Var_27 HH1 OH CZ CE 173.81 30.0 3 CME Var_28 HE2 CE CZ OH 167.31 30.0 3 CME Var_29 HE3 CE CZ OH -76.51 30.0 3 CME Var_30 HA CA N H -46.26 30.0 3 CME Var_31 HA CA N H2 73.74 30.0 3 CME Var_32 HA CA C HC1 -165.01 30.0 3 CME Var_33 HB2 CB CA HA 61.10 30.0 3 CME Var_34 HB3 CB CA HA 177.33 30.0 3 CME Var_35 HZ2 CZ CE HE2 -70.81 30.0 3 CME Var_36 HZ3 CZ CE HE2 45.43 30.0 3 CME Var_37 HZ2 CZ CE HE3 45.37 30.0 3 CME Var_38 HZ3 CZ CE HE3 161.61 30.0 3 CME Var_39 HH1 OH CZ HZ2 51.95 30.0 3 CME Var_40 HH1 OH CZ HZ3 -64.25 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign CME chir_01 CA N C CB both #

4 5

Re: [phenixbb] phenix.refine & twinning
by Nicholas Cody Sennett 19 Jan '11

19 Jan '11

Yes, it was the remark portion of the pdb. Thanks, --------------------------------------------- Nick Sennett Wood Lab, Graduate Student University of Georgia BMB Davidson Life Sciences A428 (706) 583-0303 nsennett(a)gmail.com<mailto:[email protected]> [cid:3DCE4F6D-E184-4DA2-A921-93D4311BE545] On Jan 18, 2011, at 3:00 PM, <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> wrote: I can't see any reason why this wouldn't work, but you're right, it's running untwinned ML refinement despite the twin law being set correctly. However, I just tried running the twinned example included in Phenix (the porin-twin dataset, which can be set up as a tutorial from the GUI), and it worked as expected. I'm downloading the latest installer now to double-check, but I doubt it's much different. One possibility is that the REMARK section in the input PDB file is giving conflicting instructions. Could you please run this command and send me the output (off-list, unless you're certain there isn't anything secret in there)? grep "REMARK" /Users/nick/k94e_208/Refine_30M/ligand_revised2-coot-0.pdb thanks, Nat

1 0

Post-doctoral positions at the NKI /Amsterdam to work on Autotaxin
by Anastassis Perrakis 19 Jan '11

19 Jan '11

Dear all, Post-doctoral positions are available in the Netherlands Cancer Institute in the group of Tassos Perrakis (http://xtal.nki.nl). Our group, together with that of Wouter Moolenaar and of Huib Ovaa, have a long-standing interest and lively collaboration in the function and structure of Autotaxin (ATX), a human enzyme that produces the well-established lipid mediator LPA. ATX has a very promising potential as a drug target. Together also with our collaborators at Pfizer and at Kentucky (Andrew Morris) we have recently published the structure of Autotaxin alone and in complex with our favorite inhibitor, as well as data that argue for an interaction of ATX with integrins. Structure: http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.1980.html Crystals (good fun!): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935246/?tool=pubmed Our chemistry collaborators (Ovaa group at the NKI) have also recently published data on potent inhibitors that act in vivo, as well as an activity-based probe. Best Inhibitor: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867685/?tool=pubmed Inhibitor design: http://pubs.acs.org/doi/abs/10.1021/jm1005012 Activity based probe: http://onlinelibrary.wiley.com/doi/10.1002/cbic.201000349/abstract;jsession… We are looking for highly motivated post-doctoral scientists to work on projects related to the function of Autotaxin, aiming to understand how Autotaxin activity regulates the production of LPA and how we can design more potent inhibitors and activity based probes. The project includes protein and mutant production, crystallographic studies and/ or cell biology analysis, and is funded by the KWF (Netherlands Cancer Fund) and the NWO (Netherlands Science Organization). The Netherlands Cancer Institute (http://www.nki.nl) is a center of excellence with a high standard of biological research and an interactive international atmosphere. It is located in Amsterdam, with all its cultural amenities, close to Schiphol airport. You will join a lively team, closely associated with that of Titia Sixma in the Department of Biochemistry and next to the NKI Protein facility. http://xtal.nki.nl/ http://proteinfacility.nki.nl/ The research teams at B8 are closely associated and have an interest in structural studies coupled to functional analysis, combined with activities in method development for structural biology. Our department also hosts the newly established "Protein Facility" with equipment that includes high throughput crystallization and automated crystal visualization robotics both for nano-drop and Fluidigm micro- fluidics experiments, an X-ray facility (with Micro-star Ultra source from Bruker and a MarDTB), Biacore surface plasmon resonance, isothermal titration calorimetry (ITC), static light scattering (MALLS) , Thermofluor, an automated protein expression testing platform, a mass-spectrometry unit, as well as facilities to express protein in E.coli, insect and mammalian cells. We are looking for enthusiastic researchers, which could have experience in protein crystallography and/or molecular biology and/or biochemistry and/or cell biology. Applicants should send an e-mail including a formal CV, a very short motivation letter for why they want to work on this project, and include the names of three referees, and send it to me. Tassos

1 0

Computational Crystallography Newsletter Issue 2
by Paul Adams 18 Jan '11

18 Jan '11

Dear Colleagues, I am pleased to announce the publication of the second issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to Nigel Moriarty at NWMoriarty(a)lbl.gov Articles -------- - Fuzzy space group symbols: H3 and H32 - Visualizing the raw diffraction pattern with LABELIT - Electron density illustrations - Maximum likelihood refinement for twinned structures - TLS for dummies Short communications -------------------- - Multi-criterion kinemage graphics in PHENIX - phenix.ensembler: a tool for multiple superposition - phenix.mr_rosetta: a new tool for difficult molecular replacement problems Cheers, Paul -- 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: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
by Francis E Reyes 18 Jan '11

18 Jan '11

Although I specify that I'll allow a max angle rmsd of 2.0 (angles_rmsd_max), optimize_wxc = True results in a limited range of angles.. for example my optimize_wxc output Start r_work= 0.2507 r_free= 0.2709 bonds= 0.002 angles= 0.47 r_work= 0.2558 r_free= 0.2728 bonds= 0.001 angles= 0.41 scale= 1.00 r_work= 0.2550 r_free= 0.2725 bonds= 0.001 angles= 0.41 scale= 1.40 r_work= 0.2543 r_free= 0.2724 bonds= 0.001 angles= 0.41 scale= 1.80 r_work= 0.2538 r_free= 0.2723 bonds= 0.001 angles= 0.41 scale= 2.20 r_work= 0.2533 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 2.60 r_work= 0.2529 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 3.00 r_work= 0.2525 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 3.40 r_work= 0.2520 r_free= 0.2720 bonds= 0.001 angles= 0.42 scale= 3.80 r_work= 0.2516 r_free= 0.2719 bonds= 0.001 angles= 0.43 scale= 4.20 r_work= 0.2513 r_free= 0.2719 bonds= 0.001 angles= 0.43 scale= 4.60 r_work= 0.2510 r_free= 0.2718 bonds= 0.001 angles= 0.43 scale= 5.00 r_work= 0.2501 r_free= 0.2717 bonds= 0.002 angles= 0.44 scale= 6.00 r_work= 0.2494 r_free= 0.2718 bonds= 0.002 angles= 0.45 scale= 7.00 r_work= 0.2488 r_free= 0.2716 bonds= 0.002 angles= 0.46 scale= 8.00 r_work= 0.2481 r_free= 0.2715 bonds= 0.002 angles= 0.46 scale= 9.00 r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47 scale= 10.00 r_work= 0.2561 r_free= 0.2729 bonds= 0.001 angles= 0.41 scale= 0.85 r_work= 0.2563 r_free= 0.2729 bonds= 0.001 angles= 0.41 scale= 0.70 r_work= 0.2567 r_free= 0.2730 bonds= 0.001 angles= 0.42 scale= 0.55 Final r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47 The resolution is about 1.95A and I think the angles/bonds are a little too tight. My wxc_scale is currently set to 0.01. Does optimize_wxc use this as a starting point/does it matter what this value is set to when optimize_wxc =True ? Is the scale= result in the output really wxc_scale? Thanks! F --------------------------------------------- Francis E. 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

2 3

fwd: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 18 Jan '11

18 Jan '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Tue, 18 Jan 2011 12:44:58 -0600 Subject: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, This is a reminder that the on-line applications are being accepted for the 4th annual CCP4 summer school “From data collection to structure refinement and beyond”, which will take place early June, 2011 at the APS near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

phenix.refine & twinning
by Nicholas Cody Sennett 17 Jan '11

17 Jan '11

Can phenix detwin data? I have tried to input the twinning law (l,-k,h) but phenix.refine does not create the appropriate maps and there is no appreciable change in R-factor. I have attached my xtriage and refinement logs. Thanks, Nick

3 2

Partial charges / fractional charges
by Romain Talon 17 Jan '11

17 Jan '11

Dear Phenix bulletin board users, I would like to know if there is a way to introduce a partial or a fractional charge for a given atom in a structure subjected to a refinement with phenix.refine ? It is maybe totally useless to put a charge equal to -0.5 instead of -1 for an oxygen which is involved in a non-covalent binding with an ion but I didn't found any information about that... I thank you a lot in advance. Romain. -- ----- -------- ---------------------------------------------------------- Romain TALON Extremophile and Large Molecular Assemblies Team (E.L.M.A) Institut de Biologie Structurale 41, rue Jules Horowitz 38027 GRENOBLE Cedex 1 Tel: +33 (0)438.78.95.93 ----------------------------------------------------------

3 2

Barely two weeks left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 14 Jan '11

14 Jan '11

We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

Re: [phenixbb] Refinement Problem
by Kay Diederichs 13 Jan '11

13 Jan '11

> Date: Wed, 12 Jan 2011 17:12:04 -0500 (EST) > From: Christopher W Davies<cdavies(a)purdue.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Refinement Problem > > > I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? > > > Thanks. > > Chris Chris, there is a collection of things to think about at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#R-fa… HTH, Kay

3 2

Refinement Problem
by Christopher W Davies 12 Jan '11

12 Jan '11

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? Thanks. Chris

4 6

Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

4 5

2 quesions: 1. bond and vdw restraints; 2. cif file for BeF3-
by YoungJin 11 Jan '11

11 Jan '11

Dear Phenix users, Let me ask 2 questions and, as always, thank you whoever responses. 1. First general question is regarding bond distance or van der Waals distance in the crystal structure. As I freeze the crystals as themselves , I often see those distances are much shorter than what I normally expect in the refined structure. So how far they are acceptable or do we have any reference for bonds restraints in the crystal although ccp4 library should deal with these... 2. I was trying to model BeF3-. When I tried to get restraint file from the ReadySet, it always makes BeF3 instead of BeF3-. Is there any way I can fix the charge of the molecule? Also, I would expect it should be in the library as a kind of common inorganic molecule to mimic the phosphorus group. If so, could you let me know how I can get and use it? Thanks in advance, Young-Jin

3 2

B-Factor issue
by Hasan Demirci 11 Jan '11

11 Jan '11

Hi, I am trying to refine a structure with a bound ligand "PAR". Unfortunately, input b-factor of the ligand and output values are matching exactly even tough I copied the ligand from a different structure. I manually changed the occupancy of the ligand to see if it changes the b-factor but again B-factor didn't change. Can someone help me to solve this issue? Below, I attached the first four lines of the pdb after occupancy change. input "HETATM51786 C11 PAR V 1 140.982 67.469 10.830 1.00 58.13 C HETATM51787 O11 PAR V 1 140.549 68.782 10.389 1.00 58.13 O HETATM51788 C21 PAR V 1 139.714 66.811 11.362 1.00 58.13 C HETATM51789 N21 PAR V 1 138.632 66.819 10.352 1.00 58.13 N " output "HETATM51828 C11 PAR V 1 157.285 114.375 -64.249 0.80 58.13 C HETATM51829 O11 PAR V 1 157.335 115.251 -65.379 0.80 58.13 O HETATM51830 C21 PAR V 1 158.559 113.509 -64.364 0.80 58.13 C HETATM51831 N21 PAR V 1 159.738 114.342 -64.677 0.80 58.13 N" Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

2 4

The phenix autobuilder does not find buccaneer
by Pietro Roversi 10 Jan '11

10 Jan '11

Dear all, I have Buccaneer 1.5.0: partyring:~/Projects/Japanin/autoBUSTER> $CBIN/cbuccaneer <B><FONT COLOR='#FF0000'> <html>  <hr> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 6.1: cbuccaneer version 1.5.0 : 28/05/10## ############################################################### User: pietro Run date: 10/ 1/2011 Run time: 17:18:57 and yet the phenix autobuilder fails - saying I need 1.3.0 or higher (see below) What environment variable is being checked and what should I set for the phenix autobuilder to be able to detect buccaneer? Thanks Regards Pietro **************************************** AutoBuild Input failed Sorry, the necessary version of BUCCANEER does not seem to be available.. For BUCCANEER model building you need CCP4 version 6.1.2 or higher and BUCCANEER version 1.3.0 or higher **************************************** ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Pavel Afonine [pafonine(a)lbl.gov] Sent: 07 September 2010 17:56 To: PHENIX user mailing list Subject: Re: [phenixbb] will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Hi Hailiang, > For the pdb file generated by refmac which contains only the residual-B, > will phenix.fmodel automatically generates and takes into account the TLS > B by reading the TLS REMARK from pdb? Thanks a lot! phenix.tls is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records. phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics. phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors. Pavel. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

2 1

Displaying electron density in PyMol
by Michael Thompson 09 Jan '11

09 Jan '11

Hi All, Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4? Thanks for the help, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

7 9

autobuild
by Page, Rebecca 09 Jan '11

09 Jan '11

Dear phenix community. We would like to 'fix' the residues of our current protein model, and use Autobuild (perhaps via rebuild-in-place=false, which is what we've been trying) to add missing residues to our current model . However, our efforts thus far have only resulted in models that get rebuilt from scratch. Is it possible to just 'add' residues to a current structure using Autobuild? If so, is someone could share the correct command with us, we'd be very appreciative. We can't seem to find it. Thanks in advance, Rebecca

2 1

Accessing the CCP4 monomer library in Coot opened from Phenix
by Joseph Noel 09 Jan '11

09 Jan '11

Hi All, Having trouble getting Coot loaded by Phenix to access monomers such as DTT, glycerol, etc I assume through the CCP4 monomer library. If I insert the following in the phenix file, start_coot.sh: DYLD_LIBRARY_PATH=/Applications/ccp4-6.1.13/lib:$DYLD_LIBRARY_PATH export DYLD_LIBRARY_PATH will Coot now access the monomer library? Thanks! Joe ___________________________________________________________ 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 ___________________________________________________________

2 1

Postdoctoral position at the University of Toronto
by Jinrong Min 07 Jan '11

07 Jan '11

A Post-doctoral position in chromatin structural biology is available in my group. My lab aims to characterize proteins and protein/DNA or RNA complexes by X-ray crystallography in combination with other biochemical and biophysical techniques. Applicants should have a Ph.D. in structural biology, biochemistry, molecular/cell biology with 0-4 years postdoctoral research experience. Interested candidates are invited to send their CV with 3 references to: Jinrong Min by email: jr.min(a)utoronto.ca Jinrong Min Principal Investigator, Chromatin Biology and Epigenetics Structural Genomics Consortium Assistant Professor, Department of Physiology University of Toronto 101 College St., Toronto On M5G 1L7, Canada http://www.sgc.utoronto.ca/Chromatin

1 0

error on Autobuild GUI on new version (1.7.629)
by Young-Jin Cho 07 Jan '11

07 Jan '11

Hi Phenix developers, I recently installed new version of phenix(phenix-1.7-629) FYI. I chose this installer version phenix-installer-1.7-629-intel-linux-2.6-x86_64-fc3.tar as my computer indicates 2.6.18-194.17.4.el5 x86_64 after uname -rm command. Everything was ok until I started AutoBuild program. Somehow it keeps giving me following error messages on my GUI window: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /amnt/datnew/yjcho/RUN_FILE_2.log : ImportError: numpy.core.multiarray failed to import Possibly this subprocess is run on a machine with different architecture than the main process? ******************************************************************************** *************ERROR ENDING ******************* I would thank if you can help me out from this problem. Thanks in advance, Young-Jin

3 2

anisotropic refinement gui more than one chain
by Christian Roth 06 Jan '11

06 Jan '11

Dear all, I want refine a structure with several chlorides and want refine these chlorides anisotropic. I use the GUI for the setup and manipulate the eff file just before it starts. To my surprise my constrained group definitions are used, but my anistropic refinement definitions are removed I incorporated it as followed: adp { individual { isotropic = None anisotropic = "chain a" anisotropic = "chain f" anisotropic = "chain Y" anisotropic = "chain T" anisotropic = "chain U" anisotropic = "chain z" anisotropic = "chain d" anisotropic = "chain g" anisotropic = "chain e" anisotropic = "chain V" anisotropic = "chain X" anisotropic = "chain n" } but in the log the following is stated: adp { individual { anisotropic = "chain a" } Why are all the other definitions gone? And if I defined it wrong, how I have to define it correctly? The current version I use is 1.6.4-486 Thanks Christian

3 2

CCP4 SW Web Broadcast
by ronan.keegan＠stfc.ac.uk 06 Jan '11

06 Jan '11

Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group -- Scanned by iCritical.

1 0

Questions about phenix.refine with twin_law
by Keitaro Yamashita 06 Jan '11

06 Jan '11

Dear Phenix developers, I'm working with pseudo-merohedrally twinned data (fraction 45%), using Phenix-dev-616. I have three questions about phenix.refine with twin_law. (running on the command line) During refinement with twin_law, the log file says x-ray target function is set to "twin_lsq_f". Does it mean, we cannot use maximum likelihood target for twinned data? If so, is it recommended to refine without twin_law at first several cycles? When I tried to refine using the model refined without twin_law, the target function was still ml, not twin_lsq_f although I specified twin_law. Is this a bug? When I used twin_law option, in the table "R-free likelihood based estimates", "Scale factor" were None in all resolution bins. Cannot scale factor be calculated during twin refinement? Thanks in advance and Wishing you the best holidays, Keitaro

4 16

How to get a statistics of sidechain&mainchain Bfactors?
by 商元 05 Jan '11

05 Jan '11

Dear all, I used TLS+ADP refinement to get the final structure model, after that I used phenix.model_vs_data to get the statistics for table1. However there is no B factor statistics in the output. Can I get the overall B factor by just simply averaging the B factors of each residue in the output text? Then how can I get the B factor value of the sidechains and that of the mainchain? Thanks and regards, Yuan SHANG Hong Kong

2 1

DNA covalent bond angles deviate from PDB standard dictionary
by Scott Classen 05 Jan '11

05 Jan '11

Hello, I'm running into validation problems with DNA when validating on PDB website. the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. for example, angle pdb=" O4' DG D 6 " pdb=" C1' DG D 6 " pdb=" N9 DG D 6 " ideal model delta sigma weight residual 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º What to do? Who is "right" phenix or RCSB? Thanks, Scott

3 2

bugs in dev 625
by Weiergräber, Oliver H. 05 Jan '11

05 Jan '11

Hello, trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error: ############################################ Build cycle 1 of 6 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: global name 'libtbx' is not defined Refinement failed... ############################################ If invoked directly, phenix.refine seems to run fine, so there may be a problem with scripting in the autobuild wizard. Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

3 2

viewing maps in xfit
by David Shin 04 Jan '11

04 Jan '11

Hi - Anyone have a script to convert phenix .mtz output so I can read in maps in xfit? I still find xfit handy for a few things. D

3 2

errors when disabling Rfree
by chene＠umbi.umd.edu 02 Jan '11

02 Jan '11

Dear Phenixers, I have a low resolution twinned data, for which I disabled cross validation in refinement. The refinement worked and exported the refined coordinates. However, the phs files for maps are empty and there were such errors as below. It seems the free set is required for maps. I wonder how to fix this problem? Thanks Chen Traceback (most recent call last): File "/home/chene/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 103, in run map_manger.write_files() File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1281, in write_files fmodel = self.refine_object.fmodels.fmodel_xray(), params = mtz_mc) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py", line 290, in map_coefficients_from_fmodel centrics_pre_scale = params.centrics_pre_scale) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1780, in map_coefficients w2 = w2) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1695, in map_coefficients sigmaa_object = self.sigmaa_object( detwinned_data=dt_f_obs,f_model_data=tmp_f_model, tmp_free=tmp_free,forced_update=True) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1504, in sigmaa_object kernel_width_free_reflections=200, File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 131, in __init__ raise RuntimeError("No free reflections.") RuntimeError: No free reflections. Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

3 2

Automated Mg & K ions picking
by Hasan Demirci 02 Jan '11

02 Jan '11

Hi, I have a low resolution data and I am trying to place Mg++ and K+ ions. As far as I know for ligand search at least 3 atoms required. Is it possible to do an automated search of these single atom ions by using phenix similar to automated water picking protocol? Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

2 1

MACOSX_DEPLOYMENT_TARGET mismatch between PHENIX and Coot
by Ben Eisenbraun 30 Dec '10

30 Dec '10

Howdy PHENIXians, One of my users reported this error: File "/programs/i386-mac/coot/coot-latest/lib/python2.7/sysconfig.py", line 300, in _init_posix raise IOError(msg) IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.4" but "10.5" during configure The person is running on OS X Intel, using a PHENIX nightly and trying to call Coot. It looks like the PHENIX nightlies are built with MACOSX_DEPLOYMENT_TARGET=10.4, and the Coot I built used M_D_T=10.5 and Python is unhappy about this. It's easy to test this: $ export MACOSX_DEPLOYMENT_TARGET=10.3 $ phenix.python Traceback (most recent call last): File "/programs/i386-mac/phenix/dev-606/phenix-dev-606/build/mac-intel-osx/base/Python.framework/Versions/Current/lib/python2.7/site.py", line 553, in <module> <snip> IOError: $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.3" but "10.4" during configure Or if you have access to one of our installations: $ phenix.python import os os.system('coot') Results in the original error pasted above. After playing a bit, I came up with a workaround. If you just set the M_D_T to 10.5 before starting Coot and _after_ starting PHENIX, it all seems to work. E.g. I can start Coot using this script: $ cat coot.py #!/usr/bin/env phenix.python import os os.putenv('MACOSX_DEPLOYMENT_TARGET', '10.5') os.system('coot') And since the 'coot' binary in the PATH is a wrapper script, I can just set it in the environment there. My question is: does Python actually need this? Is my workaround going to break something? I'm not enough of a Pythonista to be able to tell from looking at the sysconfig code if this will be an issue. There is a comment in the source: # On MacOSX we need to check the setting of the environment variable # MACOSX_DEPLOYMENT_TARGET: configure bases some choices on it so # it needs to be compatible. But it's not clear to me when it's going to be used. I'm almost certainly going to implement the workaround, so I'm mostly posting this for the list archives and to see if anyone has a better idea. Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

3 5

LigandFit (distorted manesium hexahydrate cluster)
by Hasan Demirci 28 Dec '10

28 Dec '10

Dear All, I am trying to run " LigandFit " with the following hydrated magnesium hexahydrate cluster (without the hydrogens) pdb. "HETATM 7 MG MG6 A 1 -53.936 117.342 91.273 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.351 117.224 89.749 1.00128.62 A O HETATM 3 O2 MG6 A 1 -52.532 117.421 92.718 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.370 118.284 92.428 1.00127.74 A O HETATM 5 O4 MG6 A 1 -53.253 119.219 90.518 1.00128.43 A O HETATM 6 O5 MG6 A 1 -54.385 115.379 91.937 1.00127.84 A O HETATM 7 O6 MG6 A 1 -52.566 116.391 89.994 1.00128.62 A O " LigandFit automatically runs the elbow and creates a new search pdb file with hydroges and while doing this, elbow totally screws up the original starting geometry of the Oxygen atoms within the cluster after the addition of hydrogens. "HETATM 1 MG MG6 A 1 -53.913 117.323 91.231 1.00128.70 A MG HETATM 2 O1 MG6 A 1 -55.140 117.947 90.141 1.00128.62 A O HETATM 3 O2 MG6 A 1 -53.080 118.061 92.589 1.00127.25 A O HETATM 4 O3 MG6 A 1 -55.453 117.480 92.061 1.00127.74 A O HETATM 5 O4 MG6 A 1 -52.768 118.528 90.669 1.00128.43 A O HETATM 6 O5 MG6 A 1 -53.676 115.727 91.923 1.00127.84 A O HETATM 7 O6 MG6 A 1 -53.363 116.194 90.004 1.00128.62 A O HETATM 8 H11 MG6 A 1 -55.461 117.161 89.473 1.00128.62 A H HETATM 9 H21 MG6 A 1 -52.333 117.378 92.967 1.00127.25 A H HETATM 10 H31 MG6 A 1 -55.430 118.350 92.700 1.00127.74 A H HETATM 11 H41 MG6 A 1 -53.300 119.422 90.378 1.00128.43 A H HETATM 12 H51 MG6 A 1 -54.636 115.255 92.077 1.00127.84 A H HETATM 13 H61 MG6 A 1 -52.319 116.372 89.793 1.00128.62 A H " Is it a bug or am I making something wrong? Does the search pdb HAVE TO be covalently linked? or can I search for a cluster? Thanks. -- Hasan DeMirci

2 1

ramachandran_restraints
by José Trincão 28 Dec '10

28 Dec '10

Dear all, I am refining a structure to 2.9 A, with pretty bad experimental data (P1, ~5400 residues in the A.U. (4 mol), anisotropic, fairly incomplete...). I have been running phenix.refine with NCS, 1 ADP per residue, lower target weights, TLS. My R/Rfree are stuck at about 2.4/3.05. I was getting around 2% ramachandran outliers at every cycle so I have been giving the nightly builds a shot. Now I get 0.2% outliers without changing any parameters for the ramachandra_restraints but it is forcing some of the peptide bonds out of the density. What can I tweak to improve the refinement? Thanks all in advance! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

3 2

Re: [phenixbb] Simple Phaser Question (Ed Pozharski
by Joseph Noel 27 Dec '10

27 Dec '10

Hi Ed, Yes, that is what I generally do but it sometimes is a slightly different so I wanted a more general approach. Joe ___________________________________________________________ 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 ___________________________________________________________ On Dec 25, 2010, at 12:00 PM, phenixbb-request(a)phenix-online.org wrote: > 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. Simple Phaser Question (Joseph Noel) > 2. Re: Simple Phaser Question (Ed Pozharski) > 3. Questions about phenix.refine with twin_law (Keitaro Yamashita) > 4. Re: Questions about phenix.refine with twin_law (Peter Zwart) > 5. Re: Questions about phenix.refine with twin_law (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Dec 2010 17:11:37 -0800 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Simple Phaser Question > Message-ID: <5E3B81ED-4C13-488E-8C28-33DB29263AEF(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible). > > Thanks and Happy Holidays! > > Joe > ___________________________________________________________ > 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 > ___________________________________________________________ > >

3 2

Simple Phaser Question
by Joseph Noel 24 Dec '10

24 Dec '10

Hi All, I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible). Thanks and Happy Holidays! Joe ___________________________________________________________ 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 ___________________________________________________________

2 1

Non-standard residue numbers in NCS restraints
by Sampson, Jared 23 Dec '10

23 Dec '10

Greetings all, My lab is working on a 3.2Å resolution structure with 6 NCS copies of an antibody Fab fragment with insertions in its CDR loops. The residue numbers of CDR loop H3, for example, include 100A, 100B, etc. in each of the heavy chains (Kabat numbering). There are observable differences between NCS copies in parts of the model due to crystal contacts and so forth, so we want to exclude those residues from the NCS. Phenix.refine, when given NCS restraints like the example below, produces a result with much higher R/Rfree values than when the same structure was run with "normal" continuous numbering (R/Rfree of .26/.30 compared to .21/.26 before changing to Kabat numbering). Reference selection: chain H and (resseq 1:100A or resseq 100H:113) Restrained selection: chain I and (resseq 1:100A or resseq 100H:113) Phenix version is 1.6.4-486. Any thoughts on what might be causing this or how to account for the non-standard numbers in NCS restraints? Thanks, Jared Sampson -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 1

Problem with Molprobity analysis in phenix 1.6.4
by Mark A Saper 22 Dec '10

22 Dec '10

I am running phenix 1.6.4-486 with GUI and obtained high clash scores in the Molprobity calculations done by phenix.refine. I think I know why after doing some experiments with the current Molprobity running at http://molprobity.biochem.duke.edu/. If I take my well-refined structure as output by phenix (.pdb) and use it directly on the Molprobity web site, the clash score is much lower: 2.75 for 39 total bumps. Many of these involve residues or waters with high B factors. If I first remove all hydrogens from the phenix-refined .pdb file with a text editor, and upload it to the Molprobity web site, then add hydrogens, and then calculate clash score, the score is now 8.69 or 123 bumps for 14150 atoms. This is *identical* to what phenix calculates. Therefore, why doesn't phenix feed the refined coordinates directly into the Molprobity (probe) calculations? Has this change been made in one of the nightly builds? Thanks, Mark Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

6 7

Fwd: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 22 Dec '10

22 Dec '10

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Wed, 22 Dec 2010 11:02:15 -0600 Subject: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, Building on the success of the past 3 years, we are pleased to announce the fourth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 7 to 15. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 8. Application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2011/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0

ADP restraints - distance power, average power, etc
by Joseph Noel 21 Dec '10

21 Dec '10

Hi All, I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)? I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2. Thanks! Joe ___________________________________________________________ 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 ___________________________________________________________

7 16

Re: [phenixbb] ADP restraints - distance power, average power, etc
by Joseph Noel 20 Dec '10

20 Dec '10

Dear Ed, Thanks so much for the suggestion about REFMAC but I seemed to have found out the issue. The positive density on Met sulfurs and backbone carbonyls and amide NHs does not appear when I calculate a "normal" sigmaa weighted mFo-dFc map. The positive density was appearing only when I checked the kicked map option. So the "extra" density seems to be due to generating kicked maps. Sorry about the confusion related to the sigma level. Just meant that the positive density was not insignificant in the kicked mFo-dFc maps. Density was visible on these specific areas starting around 3.5-4.0 sigma and visible in several places contoured up to 8 sigma. Joe ___________________________________________________________ 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 ___________________________________________________________ On Dec 20, 2010, at 12:00 PM, phenixbb-request(a)phenix-online.org wrote: > 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. ADP restraints - distance power, average power, etc (Joseph Noel) > 2. Re: ADP restraints - distance power, average power, etc > (Ralf W. Grosse-Kunstleve) > 3. Re: ADP restraints - distance power, average power, etc > (Pavel Afonine) > 4. Secondary structure restraints - where to specify file using > GUI? (Luke Rice) > 5. Re: Secondary structure restraints - where to specify file > using GUI? (Nathaniel Echols) > 6. Re: ADP restraints - distance power, average power, etc > (Joseph Noel) > 7. Re: ADP restraints - distance power, average power, etc > (Joseph Noel) > 8. Re: ADP restraints - distance power, average power, etc > (Ed Pozharski) > 9. Re: Secondary structure restraints - where to specify file > using GUI? (Luke Rice) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 19 Dec 2010 12:58:43 -0800 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] ADP restraints - distance power, average power, > etc > Message-ID: <2E132727-1B34-4ED5-98DA-2210B7D1FF48(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)? > > I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2. > > Thanks! > > Joe > ___________________________________________________________ > 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 > ___________________________________________________________ > >

1 0

phenix.refine with simulated annealing
by zhangh1＠umbc.edu 17 Dec '10

17 Dec '10

Hi there, I was trying to perform a SA refinement for PDB# 2VZ8 using the following phenix script: random_seed=2679941 phenix.refine 2VZ8.pdb 2vz8.mtz simulated_annealing=true main.random_seed=${random_seed} output.prefix=${random_seed} >${PDB}-phx-sa.log where 2VZ8.pdb was downloaded from rcsb, and 2vz8.mtz was converted from the cif file by ccp4-cif2mtz. But it ended up with: ******************* =============================== refinement start ============================== Traceback (most recent call last): File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 229, in refinement_machine xray_structure = model.xray_structure,) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 133, in extract_from_pdb_header xray_structure = xray_structure) File "/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/cctbx_project/mmtbx/f_model.py", line 302, in __init__ twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144) RuntimeError: cctbx Error: Parse error: unexpected character: NULL ************************ I tried another smaller system and it works well. Not sure what happens, and thanks for any suggestion! Hailiang

4 3

phenix.map_to_object for HA sites
by Michael Hothorn 16 Dec '10

16 Dec '10

Hi, I have a .pdb with heavy atoms that are dispersed all over the unit cell. I would like to move all of them (about 40) as close as possible to my refined structure. Could phenix.map_to_object do that for all heavy atoms at once, or would I need to do this in an atom by atom manner? Thanks Michael

2 1

Map filenames are not honored [dev-610]
by Schubert, Carsten [PRDUS] 15 Dec '10

15 Dec '10

Hi, I just noticed that v610 does not honor map file names defined in the .def file. Instead it constructs its own file name from the prefix, serial and map_type settings. That works fine for run-of-the-mill fofc and 2fofc maps, but causes a clash in map filenames when one also computes kicked maps or other maps with non-default settings beside the default fofc and 2fofc maps. Cheers, Carsten

2 1

phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Joseph Noel 15 Dec '10

15 Dec '10

Pavel or Nat, Can you point me to the button in the GUI to use to run this? I am pretty much a GUI guy although not adverse to running things through the command like like the old days (yes, I was a command like geek when I started at Yale in 1990 and until I stopped (temporarily) doing anything worthwhile around 2001. Now that I am back in the lab doing work (but probably still not worthwhile) I have become addicted to GUIs and buttons. Blame my daughters! LOL Joe ___________________________________________________________ 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 ___________________________________________________________

2 2

phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups
by Pavel Afonine 14 Dec '10

14 Dec '10

PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel.

2 2

request for openmp compile comments
by Bryan Lepore 14 Dec '10

14 Dec '10

if anyone has specifically gotten automr to run on an openmp-compiled phenix installation with something like the specs i give below, i would appreciate any details you could offer. (in my hands, automr always crashes, refine works.) -Bryan any recent nightly release with --openmp gcc/g++ 4.4.5 (or thereabouts) 2.6.35-23-generic SMP i686 (or thereabouts) amd, intel, (or thereabouts) Ubuntu (recent - but not Fedora)

1 0

phenix.refine use_experimental_phases vs target=mlhl
by Francis E Reyes 13 Dec '10

13 Dec '10

Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False? Thanks! F --------------------------------------------- Francis E. 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

6 5

AutoSol/PhaserSAD with more than one anomalously-scattering atom produces error...
by Francis E Reyes 13 Dec '10

13 Dec '10

Hi all I'm getting an error... "'InputEP_SAD' object has no attribute 'addSCAT_TYPE'" from autosol. Facts: - phenix-1.6-289 - SAD experiment with two types of anomalous scatterers in the xtal, data is the peak wavelength of one of the anomalous scatterers. - sites are input from a previous phaser run (ha_x.pdb_formatted.pdb) - the atom positions are likely correct, but the atom types are all the same atom (I'd like phenix/phaser to go through the list and reannotate/refine based on the proper heavy atom identities) - additional atom types/f'/f'' defined in autosol.eff, Using the documentation example "SAD with more than one anomalously-scattering atom" (http://www.phenix-online.org/documentation/autosol.htm). Thanks! F --------------------------------------------- Francis E. 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

2 1

changing test set flag
by Michael Hothorn 11 Dec '10

11 Dec '10

Dear all, I used phenix.refine to generate the test set flag for my dataset which it did with a value of 1. I now use a program that expects the test set flag in the mtz file to be 0. Is there a simple way to change the flag from 1 to 0 keeping the flagged reflections identical? Thanks! Michael

3 3