December 2011 - phenixbb - phenix-online.org

rosetta mr
by Shya Biswas 07 Dec '11

07 Dec '11

Hi all, I was wondering how to generate .ali file that I need to run rosetta MR. I have most of the files for the run except this one. the documentation did not help a lot. thanks, Shya

3 3

pseudo-merohedral twinning
by Zhou, Tongqing (NIH/VRC) [E] 07 Dec '11

07 Dec '11

Hi Pavel, I just collected a 2.85 A dataset with space group P212121, MR went well, however, the refinement was not fine: (eg: Rigid body r=48%, it won't go down anymore). I then ran xtriage, it turned out the my data was pseudo-merohedral twinned. The twin fraction is ~0.02. Twin_law=k,h,-l. It there a way to de-twin the data and then do the refinement or just use the twin_law="k,h,-l" at the command line? Is there a way to specify twin_fraction in the paramenter file? Also re-processed data in P41212 or P43212, the ~25% Rsym indicated the data should still be in P222. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

4 3

pdbtools
by Bradley Hintze 06 Dec '11

06 Dec '11

Developers, I am doing some automated analysis on many pdbs. My analysis is contained to a single chain in a given pdb. Aa such, to cut down on computing time I am generating many pdbs cut to the desired chain. When using pdbtools I get the following Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 46 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). Is there a way around this without creating a CIF file or another tool to cut pdbs? Thanks, Bradley -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

2 1

Rfree flag transfer
by Zhang yu 06 Dec '11

06 Dec '11

Hi, I am using phenix_1.7.1-743 GUI. I would like to transfer Rfree tag from one dataset to the other one, but had the following error, "The uni cell for the Miller array /***/*** (186.326, 103.98, 297.48, 90, 98.465, 90)" is significantly different than the output unit cell (183.486, 103.5, 295.416, 90, 98.828, 90)" Two datasets are from same kind of crystal, but with slight different cells. I guess that is why "Reflection file editor" refused to do it. Could anyone tell me how to avoid the error? Thanks Yu

2 3

autoMR wizard
by Vitali Stanevich 06 Dec '11

06 Dec '11

Hi, I'm trying to solve structure by molecular replacement. We already have structure for this protein and new is exactly the same thing with a ligand soaked. I can solve it without a problem with ccp4 gui (tfz=47.7), but not with phenix.automr, which is disappointing. Can somebody point me out what's wrong with my data input? I did it with this command: phenix.automr output.sca complex_search.pdb identity=90 mass=93500 copies=1 or with .eff file (attached) Thanks, Vitali

2 1

H related bond deviaion
by Dialing Pretty 06 Dec '11

06 Dec '11

Dear All, I did a Phenix refine, and before the refine all the H were added. MolProbity analysis demonstrated that almost everything are acceptable after the refinement. However when I did the geometry analysis by the COOT validation, I find all the residues having a significant deviation bond involving H. with z score higher than 7. I am looking forward to getting an explanation from you on it,including how to avoid it. Cheers, Dialing

3 2

bond deviation deected by Coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, After Pheneix refine, the quality of the structure improved significantly as analyzed by Molprobity. However the bond deviation increased significantly after the refinement. Will you please tell me which refine function can be used to reduce the bond deviation detected by the Coot geometry analysis? Cheers, Dialing

3 3

rotamer outlier reduction by coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, I am leaning rotamer outlier reduction by Coot. After select a rotamer and acception, I find some hydrogens in the outlier rotamer will be isolated from the rotamer, and the rotamer will have new hydrogens at its new position. Is any influence by further refine by phenix? After new rotamer acception, I have did the rotamer auto-fit, I find there is a trend on that several oxygens can pack together. How to process this problem? After I save the new PDB file by coot after I selected the new rotamers to replace the outlier rotamers, I did a Phenix refine. There is an error message at the start says "Number of atoms with unknown nonbonded energy typensymbol: 2228". What does it mean and how to solve the problem? Is any simple method by which I can do the rotamer outlier reduction by Coot? I am looking forward to getting your reply. Dialing

3 2

documents explaining parameter settings in phenix-1.7.2
by Ruan Wenjie 05 Dec '11

05 Dec '11

Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie

6 9

Job Opportunity - Head of the Berkeley Center for Structural Biology
by Paul Adams 04 Dec '11

04 Dec '11

The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0