- phenixbb - phenix-online.org

Double stranded DNA restraints?
by Rajagopalan, Senapathy 02 Apr '10

02 Apr '10

Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

1 0

Secondary structure restraints for nucleic acids
by Peter Grey 02 Apr '10

02 Apr '10

Dear developers, Does the new mechanism of secondary structure restraints apply to nucleic acids as well ? Are the average bond distances similar and does DSSP works well with RNA/DNA ? Thank you in advance for clarifying this issue, Peter.

2 2

Installation problem
by Tatsuya Kaminishi 02 Apr '10

02 Apr '10

Dear Phenix BB When I tried to install the latest binary version (1.6.1), the "install" script always stopped and dumped an error message as follows: ----- /software/PHENIX/phenix-installer-1.6.1-357/bin/install-from-binary: line 347: 10964 Floating point exception$PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py -- current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >> $PHENIX_LOG/binary.log 2>&1 Error configuring: see /software/PHENIX/phenix-installer-1.6.1-357/ build-binary/intel-linux-2.6-x86_64/lupus/log/binary.log for details ----- And this "binary.log" file looks like this; ========== . . After many lines... . ./reduce/comment_out_carboxylate_H_v2.3.pl ./reduce/Makefile ./reduce/libtbx_refresh.py ========== This never happened when I installed version 1.6-289. Could anybody out there tell me how I can get around this? Or anything important is missing? The system I'm using is: Linux crux 2.6.16.60-0.27-smp #1 SMP Mon Jul 28 12:55:32 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux SUSE Linux Enterprise Desktop 10 (x86_64) VERSION = 10 PATCHLEVEL = 2 Thank you very much for your help in advance! Best regards, kami Tatsuya KAMINISHI, Ph.D. Fucini Laboratory Institute for Organic Chemistry and Chemical Biology Johann Wolfgang Goethe University Max-von-Laue-Strasse 7, N160/B413 D-60438 Frankfurt am Main, Germany Tel: +49 69 798-29165 Fax: +49 69 798-29268 Web: http://user.uni-frankfurt.de/~joharms/akfucini/

2 1

Restraints on dihedrals in phenix.refine
by Gregers Rom Andersen 02 Apr '10

02 Apr '10

hi phenix-bb in the standard phenix.refine scripts there are options for adding user defined restraints on bonds and angles, but not on dihedrals. Is this currently possible in phenix.refine? One application would be to restrain the phi-psi angles of a low resolution structure to phi-psi angles from a high-res structure of the same protein, an option previously made possible for xplor in the USF program XPLO2D gregers Gregers Rom Andersen Associate professor Department of Molecular Biology University of Aarhus Gustav Wiedsvej 10C DK8000 Aarhus C phone +45 89425024 fax +45 86123178 www.bioxray.au.dk/gra

3 2

Cadmium missing atoms
by Kristin Sutton 31 Mar '10

31 Mar '10

Hello- I am refining a structure with 2 cadmium ions present. From the extensions menu in coot, I clicked on modeling >> residues with missing atoms, and both Cadmium ions came up in that list. The density surrounding these atoms is also strange, positive density right in the middle of the atom, negative density surrounding the whole atom. How do I make sure these are being refined correctly? Thank you in advance, Kristin ******************************************************************** Kristin A. Sutton Graduate Student University of Buffalo Department of Structural Biology Hauptman-Woodward Medical Research Institute 700 Ellicott Street Buffalo, NY 14203 P: (716)898-8683 F: (716)898-8600 E: ksutton(a)hwi.buffalo.edu

3 3

Phenix version 1.6.1 released
by Paul Adams 31 Mar '10

31 Mar '10

The Phenix developers are pleased to announce that version 1.6.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.1) are: - Fast automated rotamer fixing in phenix.refine - Use of atomic charge in calculation of scattering factors - New Graphical User Interfaces for phenix.superpose_pdbs, phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, and phenix.fmodel - Consolidated validation tool in GUI - New map calculation tool, phenix.maps (also used in GUI) - Rapid loading of structures in GUI selection editor - Improved geometry restraints to maintain amino acid rotameric states - Alpha version of secondary structure restraints - Automated secondary structure analysis with KSDSSP (code from UCSF CGL) For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that 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 Acting 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: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

1 0

Re: [phenixbb] Citation for xtriage
by Folmer Fredslund 30 Mar '10

30 Mar '10

Dear Mark, On 30 March 2010 19:30, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > > I'm writing up some results for which we used phenix.xtriage to screen xtals > for twin fraction and would like to know if there is a paper we could/should > cite? > > At the time this work was done we were not using the rest of the phenix > suite for refinement (we are now!). > Going to the phenix FAQS (http://www.phenix-online.org/documentation/faqs.htm#anch2) it would be 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. Echoo ls, 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). Or maybe the developers prefer you cite the CCP4 newletters listed at: http://www.phenix-online.org/documentation/xtriage.htm#anch24 Hope this helps, Folmer Fredslund

1 0

Citation for xtriage
by Dr. Mark Mayer 30 Mar '10

30 Mar '10

I'm writing up some results for which we used phenix.xtriage to screen xtals for twin fraction and would like to know if there is a paper we could/should cite? At the time this work was done we were not using the rest of the phenix suite for refinement (we are now!). Thanks, Mark --

1 0

shaking a PDB without introducing clashes
by Francois Berenger 30 Mar '10

30 Mar '10

Hello, I recently used "phenix.pdbtools modify.sites.shake=..." in order to have some data from 0.1 to 5A. away from the true structure in order to test some scripts. I think this introduced clashes in the "shaken" PDBs I got. Is there a tool/way to avoid this? Best regards, Francois.

4 5

RMSD Dihedrals
by J. Fleming 30 Mar '10

30 Mar '10

Hi all, I'm working on a ~3 angstrom structure of a protein with approximately 800 residues. The structure is mostly helical with interspersed turns. I've been using Phenix exclusively for the refinements and have a model that I believe to be pretty good with the exception of the dihedrals (see attached). I've looked at and employed some of the general suggestions for low resolution structures here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#Refi… I tried using "discard_psi_phi=False" but it only resulted in a change dihedrals of +0.10 with minimal changes to Ramachandran outliers. I'm unsure how to proceed and would love to hear any thoughts/opinions/suggestions. Thanks for all the help! -Jon

2 1