- phenixbb - phenix-online.org

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.

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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 #

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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

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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

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Computational Crystallography Newsletter Issue 2
by Paul Adams 19 Jan '11

19 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 ] --

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phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
by Francis E Reyes 19 Jan '11

19 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

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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

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phenix.refine & twinning
by Nicholas Cody Sennett 18 Jan '11

18 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

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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 ----------------------------------------------------------

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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) =========================================================================

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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

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Refinement Problem
by Christopher W Davies 13 Jan '11

13 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

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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

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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

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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

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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

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Displaying electron density in PyMol
by Michael Thompson 10 Jan '11

10 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

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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

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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 ___________________________________________________________

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Postdoctoral position at the University of Toronto
by Jinrong Min 08 Jan '11

08 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

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error on Autobuild GUI on new version (1.7.629)
by Young-Jin Cho 08 Jan '11

08 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

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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

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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.

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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

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How to get a statistics of sidechain&mainchain Bfactors?
by 商元 06 Jan '11

06 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

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