- phenixbb - phenix-online.org

Phenix version 1.7 released
by Paul Adams 26 Jan '11

26 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 24 Jan '11

24 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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