- phenixbb - phenix-online.org

cis peptides
by Timothy Springer 30 Jan '11

30 Jan '11

Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA? Tim

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Re: [phenixbb] Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 30 Jan '11

30 Jan '11

Hi Pavel! Thanks for the reply. It does seem to be working though in the current version as long as I choose advanced level in the gui. Does it make sense though that it is lowering my Free-R? Also, the upshot is that the Fo-Fc maps are much flatter. I can see waters to build but only in the 2Fo-Fc sigmaa weighted maps so it does certainly seem to be doing something. Anyway, I look forward to the docs on it when you officially release it. Seems useful! Best- 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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selection string for omit maps
by Alexandra Deaconescu 29 Jan '11

29 Jan '11

Hi: I am new to Phenix and I am currently using the GUI. I would like to compute a sa-omit map by leaving out residues 204-209 of my chain C. In the GUI, what is the proper syntax for this selection string? I tried a few obvious formats but the jobs failed. Thank you very much in advance, Alexandra ----- Original Message ----- From: phenixbb-request(a)phenix-online.org To: phenixbb(a)phenix-online.org Sent: Tue, 25 Jan 2011 15:00:01 -0500 (EST) Subject: phenixbb Digest, Vol 62, Issue 25 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. Problem with loop fitting (Kendall Nettles) 2. Re: Problem with loop fitting (Tom Terwilliger) 3. Re: Problem with loop fitting (Kendall Nettles) 4. Ligandfit bug report (Kendall Nettles) 5. Re: Ligandfit bug report (Nigel Moriarty) 6. ADP: fix_wxu and wxu_scale (fulvio saccoccia) 7. Re: Problem with loop fitting (Tom Terwilliger) 8. Re: ADP: fix_wxu and wxu_scale (Pavel Afonine) 9. Re: adp values (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Mon, 24 Jan 2011 15:47:02 -0500 From: Kendall Nettles <knettles(a)scripps.edu> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Problem with loop fitting Message-ID: <C9634F76.F559%knettles(a)scripps.edu> Content-Type: text/plain; charset="iso-8859-1" Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: "No suitable gap found matching residues" I'm not sure what the problem is. Best regards, Kendall Nettles knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A # fit_loops # # Fit loops in a PDB file with gaps # Type phenix.doc for help Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT No suitable gap found matching residues 331 - 336 chain: A No final model obtained

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Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 29 Jan '11

29 Jan '11

Hi All, Does it make sense that when the box for "use statistical model for missing atoms" is picked under the GUI's "Global refinement parameters options" that one might obtain "better" Free-R values? I seem to be seeing that for a 2.3 A refinement of a crystal with a monomer of 550 residues in the asymmetric unit and 68% solvent content. When I uncheck the box I get about a 3% increase in Free-R. Is there more information about what this option is actually doing and when it might be useful to employ? 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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REMINDER - EMBO 2011 Practical Course - ESRF-EMBL, Grenoble, France, 6 - 10 June 2011
by Daniele de Sanctis 28 Jan '11

28 Jan '11

Hi all, Just a reminder, as deadline is approacing DEADLINE TO APPLY FEBRUARY 28th COURSE ANNOUCEMENT EMBO 2011 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 6 - 10 June 2011 The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 6 to 10, June 2011. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. The number of participants is limited to 20 and the deadline for application is February 28th, 2011. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://cwp.embo.org/pc11-03/ -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Carien Dekker is out of the office.
by carien.dekker＠novartis.com 27 Jan '11

27 Jan '11

I will be out of the office starting 01/27/2011 and will not return until 01/31/2011. I will respond to your message when I return.

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Phenix version 1.7 released
by Paul Adams 27 Jan '11

27 Jan '11

The Phenix developers are pleased to announce that version 1.7 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface ------------------- - Simplified AutoMR interface for single-component searches. - Multi-criterion validation kinemage display in KiNG. - Validation of RNA, isotropic ADPs, occupancies. - Improved project management interface, which will automatically import old projects to the new format when upgrading from a previous version of Phenix. - Integrated help browser on Mac with contextual help buttons embedded in program windows. - phenix.find_tls_groups available as part of the phenix.refine GUI. - Improved and expanded documentation for wizard and Phaser GUIs. Structure refinement -------------------- - A new fast real space refinement protocol, which can substantially improve poor starting models. - A fast method for automated identification of TLS groups (phenix.find_tls_groups). - Reference model, Ramachandran, and secondary structure restraints to improve refinement at low resolution. - Automated secondary structure restraint generation for non-Watson-Crick base pairs (using the Saenger classification). - Automatic support for D-peptides when using standard PDB residue names. Molecular Replacement --------------------- - A new command, phenix.mr_rosetta, which integrates molecular replacement, automated model building and Rosetta model rebuilding for difficult structures. - A new fast search method in Phaser for efficiently locating multiple copies of the same molecule - A new program (mr_model_preparation) for preparing models for molecular replacement, which automatically downloads related molecules based on a sequence alignment and runs sculptor. - Improvements to ensemble generation (phenix.ensembler), with an option to use secondary structure matching (using code from Eugene Krissinel). Ligand fitting -------------- - New tool for automated ligand fitting using previous structures of related protein/ligand complexes (phenix.guided_ligand_replacement). - Bug fixes and other improvements to phenix.elbow. Analysis -------- - Multi-criterion kinemages can now handle custom restraints (from a .cif file). - RNA model validation is now available on the command line (phenix.rna_validate). - Updates to phenix.model_vs_data, which now generates Sigma-A plots and more detailed ADP statistics. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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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adp values
by Agnieszka 25 Jan '11

25 Jan '11

Hello, I have 1.96 resolution structure (RNA) which I refine with individual adp factors. I found that in some cases the differences of apd between the covalently bonded atoms is quite large, for example: phosphate 24 and one of the oxygen 33; O4' - 26 and C1'-18. In extreme case for the so4 anion is: sulphate atom 63 and one of the oxygen 31. Why is it happened? I was trying refmac and the b-factors are totally different (they are much bigger). Is it because of scaling and resolution? thank you in advance, Agnieszka Kiliszek

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ADP: fix_wxu and wxu_scale
by fulvio saccoccia 25 Jan '11

25 Jan '11

Dear Phenix users and developers, I'm trying to refine a 3 A resolution structure. In order to better understand how can I use wxu_scale and fix_wxu options in phenix.refine, may you explain me their use, since I have a lot of problems with ADPs? In fact, I have big variations between atoms of the same residue. So, is it better to use wxu_scale or to impose fix_wxu to refine the ADPs? Thanks to all Fulvio Saccoccia

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Problem with loop fitting
by Kendall Nettles 25 Jan '11

25 Jan '11

Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: "No suitable gap found matching residues" I'm not sure what the problem is. Best regards, Kendall Nettles knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A # fit_loops # # Fit loops in a PDB file with gaps # Type phenix.doc for help Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT No suitable gap found matching residues 331 - 336 chain: A No final model obtained

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Ligandfit bug report
by Kendall Nettles 25 Jan '11

25 Jan '11

We are generating pdb files with chemdraw3D, which turn out to not be "real" pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers blank, such as Oxygen #2, and Carbon #18: HETATM 17 C16 LIG 1 -83.510 -0.856 0.582 1.00 20.00 C HETATM 18 O01 LIG 1 -86.640 -2.401 -0.357 1.00 20.00 O HETATM 19 O LIG 1 -75.199 2.925 2.145 1.00 20.00 O HETATM 20 C17 LIG 1 -83.058 -0.188 1.872 1.00 20.00 C HETATM 21 C LIG 1 -76.676 0.780 -1.835 1.00 20.00 C After editing it to add in the missing numbers, I re-ran elbow, and found that the resulting optimized ligand had imploded, producing altered atom connectivity. If I ran it with --final_geometry it came out OK. If you would like files to reproduce the error, I am happy to send them. Best, Kendall Nettles

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autobuild and buccaneer reference
by Bryan Lepore 21 Jan '11

21 Jan '11

1.7-629 it appears that autobuild does not have buccaneer implemented such that _buccaneer's_ reference structure method is used - N.B. i do not mean the "reference structure" as used by resolve/autobuild. any comment appreciated, thanks -Bryan

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Stereochemistry statistics
by miket＠chem.ucla.edu 20 Jan '11

20 Jan '11

Hi All, I have a very naive question, but nobody I have asked has been able to give me a confident answer. When phenix calculates the stereochemistry statistics for a model, two of the statistics given are RMS(chirality) and RMS(planarity). What specific measurements are being calculated to produce these statistics, and what are the units for the numbers given? For example, is RMS(planarity) telling me the average distance out of plane for an atom that should be in plane? If this is the case I imagine the units are angstroms? Thanks for the explanation, 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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Ten days left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 20 Jan '11

20 Jan '11

This may be the last reminder that 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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Submitting autobuild to cluster
by Kendall Nettles 20 Jan '11

20 Jan '11

Dear PHENIX developers, I'm preparing a bunch autobuild runs. If I submit 20 autobuild jobs to our 100 node cluster, what would you recommend for nproc and nbatch? How about for 10 jobs at once? Thanks! Kendall Nettles

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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

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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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