- phenixbb - phenix-online.org

Creating files with positive and negative map peaks
by Jennifer Ekstrom 23 Jul '08

23 Jul '08

I would like to obtain a file with a listing of positive and negative difference map peaks, similar in formatting and content to the files that would come out of cns: positive peaks in: <output_root>_positive.peaks negative peaks in: <output_root>_negative.peaks We need this for use in DDQ at the jcsg validation server (http://www.jcsg.org/prod/scripts/validation/sv2.cgi). Is there an easy way to create these peak files in phenix.refine? We'd prefer to not re-refine in CNS as we have *many* alternate conformations... Thanks, Jennifer

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NCS constraints in phenix.
by colletier 19 Jul '08

19 Jul '08

Dear All Does a beta version of phenix.refine that would allow the use of NCS constraints exists somewhere ? Best Jacques Ph Colletier

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SIR with sites from SAD?
by Francis E Reyes 17 Jul '08

17 Jul '08

I have a SAD dataset where autosol was able to find sites, but the resulting density modified map was uninterpretable. The unit cell for this SAD set was Unit cell: (53.2373, 53.2373, 186.446, 90, 90, 90) . I now have a heavy atom derivative. What's the format of autosol.inp (to be passed to phenix.runWizard AutoSol) that allows me to use the heavy atom sites from the SAD set as a basis for helping find heavy atom sites in the heavy atom derivative? Is it the same as SIR, except use ha_sites_file for the SAD solution? Native unit cell: [53.155600000000007, 53.1556000 00000007, 187.37970000000001, 90.0, 90.0, 90.0 Derivative unit cell: [53.1 82299999999998, 53.182299999999998, 187.59569999999999, 90.0, 90.0, 90.0]. Thanks FR --------------------------------------------- Francis 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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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 16 Jul '08

16 Jul '08

I will be out of the office starting 07/16/2008 and will not return until 07/21/2008.

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Anomalous difference map calcluation
by Jendrek 16 Jul '08

16 Jul '08

Dear All, I'm looking at my anomalous difference map from phenix.refine and it seems more or less random distributions of electron density peaks. I know that the signal is there since I solved it with SAD. I'm using I(+/-) for refinement and everything seems to work fine except the map generation. The only thing that worries me is that during the creation of _data file for refinement DANO column was not preserved. Is it necessary for phenix.refine in order to generate the anomalous difference map? How can I make sure that the DANO column is preserved (if necessary)? And by the way why is anomalous map file not generated just coefficients in the mtz? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940

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Postodoctoral Position - Berkeley California
by Paul Adams 14 Jul '08

14 Jul '08

The Berkeley Center for Structural Biology (BCSB) has an opportunity for a Postdoc to develop hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. You will also provide technical and scientific help to users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California and participate on projects involving the structure determination of biological molecules and biomolecular complexes as required by users and other BCSB staff members. Responsibilities Under the direction of the Principal Investigator, you will: - Assist in the development of hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. - Participate in engineering projects to advance the capabilities of the beamlines, including robotics systems for sample handling. - Assist in the development of instrumentation and methodology for biological crystallography. - Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. - Participate in helping users regarding data collection, processing, archiving, and analysis. - Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. - Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. - Provide work oversight and direction to technical staff as needed (which will require occasional work off-hours and weekends). - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. Key Qualifications - A recent Ph.D. in physics, biology, bioengineering, biophysics, or related field. - Experience working in the area of synchrotron science using complex instrumentation and computer controls. - Experience with robotics hardware and control systems. - Experience with the collection of experimental data for biological crystallography. - Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. - Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. - Experience in the use of computer programs required for biological crystallography. - The ability to work in a team environment and effectively interact with a broad range of colleagues. - Experience in UNIX computing is highly preferred. This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. How To Apply To apply please visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21987&p=1 Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce. -- 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. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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broken bonds in the substrate
by houjin zhang 11 Jul '08

11 Jul '08

Hi: I am trying to use phenix.elbow to generate restrains for a substrate. I notice that the PDB file produced by elbow contains some broken bonds. So I ran the elbow with the internal strings ATP. The output PDB file also harbors broken bonds. The --opt did help a little. But some bonds still look weird. I am wondering if this a bug or I just didn't install phenix right. I use the latest version of phenix and default setting. Thank you very much!! Houjin

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Reminder: Crystallographic Computing School registration deadline approaching
by Ralf W. Grosse-Kunstleve 11 Jul '08

11 Jul '08

The registration deadline for the 2008 Crystallographic Computing School is in two weeks: *** July 25 *** The schedule of the program including abstracts from all speakers is available here: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html This program puts a strong weight on fostering one-on-one interactions. There will be only 16 lectures of 45 minutes each (12 hours total) but more than 20 hours of tutorials and demonstrations. Don't miss this unique opportunity for close interaction with the developer community! On behalf of the organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)

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PHENIX on OS X Intel 10.5 "need access to screen" error
by Ben Eisenbraun 10 Jul '08

10 Jul '08

Howdy, I have PHENIX 1.3-rc2 built on an OS X Intel 10.4 machine. It runs fine there, but using the same installation mounted via NFS, I get this error: This program needs access to the screen. Please run with 'pythonw', not 'python', and only when you are logged in on the main display of your Mac. I dug around in the program a bit to see if there was a script testing for the DISPLAY setting, but this seems to be generated in the wx-python bits: build/mac-intel-osx/base/Python.framework/Versions/2.5/lib/python2.5/site-packages/wx-2.8-mac-ansi/wx/_core.py contains the error message, as do a couple of other files in the /wx/ hierarchy. The PHENIX 1.3-rc2 I built on OS X 10.4 PPC works fine on the 10.5 PPC machines, so I'm a bit surprised it's failing on the Intel side. Does anyone know if a PHENIX built on 10.5 will work on a 10.4 machine? If it was really necessary, I could install versions built on both 10.4 and 10.5, but I'd prefer to avoid it if possible. Any insight on fixing this would be much appreciated. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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Re: [phenixbb] phenix.autobuild: command not found
by Paul Adams 09 Jul '08

09 Jul '08

Hi, Please install the latest version of Phenix (1.3-rc2) from the web page. Cheers, Paul On Jul 8, 2008, at 6:45 PM, Vinayak Agarwal wrote: > Hello, > > I installed Phenix 1.24 on Fedora 8 and get the following error > message while trying to use phenix.autobuild command on the command > line: > > bash: phenix.autobuild: command not found > > Could you please help me to rectify this? > > When I try to run the GUI by typing in phenix at the command line, I > get the following warning messages, though the GUI does open: > > Shell variable SSH_PATH not set > > Shell variable RSH_PATH not set > > Thanking you, > > Sincerely, > > Vinayak Agarwal -- 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. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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