- phenixbb - phenix-online.org

wilson scale
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, For my structure, the wilson scale is 0.5, is it fine or not? Best regards. Dialing

2 1

phenix.superpose_pdbs and nucleic acids.. does it work?
by Francis E Reyes 14 Dec '11

14 Dec '11

Hi phenixer's. I need to do a superposition of two pdbs. I guess phenix.superpose_pdbs is my jiffy but it doesn't seem to work for nucleic acids (tried selection = 'name P' or selection = 'all'). LSQKAB seems to have the same limitation. They are the exact same PDBs (1 to 1 atom/residue mapping) but just shifted and rotated relative to the other. I need a superposition or the transformation matrix for all atoms. Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 450, in <module> run(args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 434, in run m = manager(params.extract(), log) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 171, in __init__ selection_moving = self.selection_moving) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 306, in _alignment "bugs(a)phenix-online.org for help.") RuntimeError: Failed to identify corresponding atoms from sequence alignment. This is probably a bug - contact bugs(a)phenix-online.org for help. I may just strip it down to phosphate's and rename the residues to ALA but a quick phenix jiffy would be great. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

on residue bond deviation
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, After a key step refinement byPhenix refine, I find there are 2 residues (total about 450 residues) with bad angles as analyzed by MolProity (deviation ratio 0.46%, goal is 0.1% ), both of the 2 residues are Pro, and both of the deviation angles are C-N-CA. Will you please give the comment on what do the 2 deviations mentioned above mean for my whole protein structure, or should I continue to refine my protein structure? I am looking forward to getting your reply. Dialing

2 1

on the input file for the Phase and build
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, For the Phenix Phase and build, the input mtz file is the scala mtz file, and the ouput mtz file will be the mtz file with phase, is this correct? I am looking forard to getting a reply from you. Cheers, Dialing

2 1

strange MR problem
by intekhab alam 12 Dec '11

12 Dec '11

Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 4

Phenix version 1.7.3 released
by Paul Adams 12 Dec '11

12 Dec '11

The Phenix developers are pleased to announce that version 1.7.3 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: ==================== - New GUIs: MR-Rosetta - viewer for diffraction images (also available as phenix.image_viewer) - editable heavy-atom sites in HySS and AutoSol General: ======== - New commands: phenix.ncs_average, phenix.model_vs_sequence, phenix.image_viewer, phenix.find_alt_orig_sym_mate, phaser.MRage - support for CNS v1.3 reflection files Refinement: =========== - Reduced memory requirement for map related calculations - Improved handling of parameter files in the GUI - RNA geometry target now includes pucker & base type-specific Chi 1 parameters - TLS group definitions from PDB file header will be automatically used if no groups are provided by the user - Bug fix in clashscore calculation for large structures with duplicate chain IDs plus SEGIDs - Torsion NCS restraints uses SEGIDs if present in input PDB file Molecular Replacement: ====================== - phaser (version 2.4): - support for pseudo-translational non-crystallographic symmetry (tNCS) in molecular replacement - detects presence of tNCS from inspection of native Patterson - characterizes tNCS parameters (translation, small rotational difference between copies) - accounts for effect of tNCS in molecular replacement calculations - note: support currently limited to one tNCS operator relating two molecules (or sets of molecules) - FAST search method turned on by default, replacing FULL search method - MR possible with a model containing a single atom - B-factor refinement turned on by default in molecular replacement - Bug fix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux - Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position - phaser.MRage (version 0.1.0) - automated MR: - New command-line switches for common actions, e.g. setting the verbosity, getting PHIL parameters, etc - Define component by sequence, but calculate molecular weight from available models if sequence is omitted - Calculate number of copies to find from Matthews coefficient - Ability to perform homology search (currently only BLAST is supported, either local installation or NCBI service) - alignments automatically generated for "template" if target sequence is known - various options for queueing systems, e.g. qslot - option to automatically write out solutions - fully parallel space group exploration - phenix.find_alt_orig_sym_mate (new command): - For different molecular replacement solutions from the same dataset, finds the copy of moving_pdb closest to reference_pdb with respect to all symmetry operations and alternative origin shifts permitted by the spacegroup in moving_pdb Experimental Phasing and Model Building: ======================================== - AutoSol: - Fixed problems with clean_up=True deleting overall_best.pdb - Allow data file names of any length - Use NCS in scoring by default if ncs copies > 2 - Correct anisotropy and sharpen by default - AutoBuild: - Automatic anisotropy correction and sharpening for all maps - phenix.multi_crystal_average: - Automatic anisotropy correction and sharpening - Automatic filling of reflections to highest resolution of any dataset - Masking heavy-atom sites from averaging - Inputs grouped by crystal Miscellaneous: ============== - phenix.ready_set/phenix.reduce: - Improved handling of alternate conformations - phenix.cif_as_mtz - Support for files containing multiple datasets - Extraction of Hendrickson-Lattman coefficients and anomalous arrays - New map_to_asu and remove_systematic_absences options - phenix.maps: - Added atom selection parameter for simple omit maps (omit.selection) - phenix.ligand_identification: - Implemented methods to generate custom ligand library based on parent protein's SCOP or CATH terms, Pfam accession numbers, GO accession numbers, or InterPro ID - Improved ligand geometry after real-space refinement 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 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

ncs_average output map
by Ursula Schulze-Gahmen 12 Dec '11

12 Dec '11

I am puzzled about my ncs-averaged output map. I determined the ncs relation using phenix.find_ncs with pdb and mtz input. The program finds 2 NCS groups with 3 molecules each and the rmsds are low. I then read in the ncs_spec file and an mtz file with map coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT coefficients. The output map seems cleaner than the unaveraged map and shows some of the same features, but the density around the 3 molecules is not identical. 2 of them look very similar, but the density around one of them is somewhat different. How is this possible if the map is averaged? Thanks for any suggestions or explanations. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

2 3

AutoBuild Question
by Page, Rebecca 12 Dec '11

12 Dec '11

Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca

4 4

phenix.refine_failed
by Xue-Yuan Pei 12 Dec '11

12 Dec '11

Dear Phenix Experts: My phenix.refine has developped the following error (see below). I tried to check my PDB format, there is not B-factor error. so what could be wrong that stoped my phenix.refine without PDB and .def files in the output? Many thanks for your advice. Xue yuan Pei, Ph.D Department of Biochemistry University of Cambridge Cambridge CB2 1GA U.K > Error messages: > Traceback (most recent call last): > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", > line 105, in run > refine_object.write_refined_pdb(f_pdb) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", > line 1284, in write_refined_pdb > ignore_hd = not self.neutron_refinement) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 534, in __init__ > ignore_hd = ignore_hd) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 449, in __init__ > molprobity_scores=True) > File "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model.py", > line 1063, in geometry_statistics > molprobity_scores = molprobity_scores) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 112, in __init__ > self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/validation/clashscore.py", > line 167, in analyze_clashes > stdin_lines=tmp_r.as_pdb_string()) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/iotbx/pdb/hierarchy.py", > line 527, in as_pdb_string > siguij=siguij) > RuntimeError: atom B-factor does not fit into F6.2 format: > "ATOM 1 N GLY A 1 " > B-factor: 111147.29 >

3 3

phenix.refine_failed
by Christian Roth 12 Dec '11

12 Dec '11

Hi, indeed your B-Factor shown in the error message for Gly A 1 is unrealistic. Is maybe in your pdb-file a space missing? I think a 8 digit B-Factor is not possible in the pdb format. Best Regards Christian

1 0

Phaser not writting out ligands
by Yarrow Madrona 09 Dec '11

09 Dec '11

Hello, I am having trouble with Phaser not writing out my ligands (HEME and small molecule) to it's output PDB even though they are in the input PDB. I am running through the GUI using Phenix version 1.7.3-921. Phenix refine recognizes HEME from the CCP4 library I think so I am not sure why I at least do not get a HEME in the output PDB. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 1

Please apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 09 Dec '11

09 Dec '11

We are offering RapiData 2012, the fourteenth 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 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students 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 tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 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, Sonya Kiss, 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) =========================================================================

1 0

map output from ncs_average
by Ursula Schulze-Gahmen 09 Dec '11

09 Dec '11

I used ncs_average to create an averaged fo-fc map. From the manual I thought that the output map is a CCP4 map. I have however difficulties to read it into Pymol as ccp4 map. It is not recognized. Any suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

3 4

print_sequence
by Bradley Hintze 09 Dec '11

09 Dec '11

Hi, I am analyzing many PDBs vai a script. Thus, I am feeding print_sequence the full path of the given PDB. This has the unfortunate effect of having a filename more than 80 char. As such the '>filename' line is split into two lines making parsing less than ideal. Is there a way I can avoid having the full path on the '>' line and still give print_sequence the full path? Or can that feature be added? Thanks, -- Bradley

2 1

excluding atoms from refinement
by Crystal VanderZanden 08 Dec '11

08 Dec '11

Does anybody know if there a general code that will allow us to exclude something from refinement? I would like to specify that there is a particular part of my structure that I don't want to refine the position. I've thought about deleting those atoms from the pdb file, but then that phasing information is excluded from the refinement. Any ideas? Thanks, Crystal

3 2

Re: [phenixbb] Autosol problems
by Tom Terwilliger 08 Dec '11

08 Dec '11

Hi Stacy, I'm sorry for the trouble! Normally autosol should not have problems with resolve, so this indicates that either (1) the data are unusual or (2) there is some problem in autosol. Can you possibly send along (terwilliger(a)lanl.gov) the log file from autosol and the LAST.log file if there is one? Also what version of phenix is this? (type "phenix.version") Thanks! -Tom T On Dec 8, 2011, at 8:55 AM, stacy William wrote: > Dear All... > I am new user for Phenix. I am right now working with SAD data. I had run Ausol in GUI interface with my SAD anamolous data. but when i am using the output file for my autobuild program it is giving problems with Resolve... n terminating with an error message suggesting to check resolve file. Do i need to change some parameters in Autosol to produce right output files which in turn can work as input files for Autobuild program > Thanks > Stacy > > Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

1 0

automr wizard: searching for all plausible space groups option
by Vitali Stanevich 08 Dec '11

08 Dec '11

Hi, I'm trying to solve structure by MR with phenix 1.6.1-357 version. I have 100% identity search model and can find solution without problem in ccp4i in P212121 sg. But, I can't do it in phenix.automr command line because program looks only for P222 space group (pointed out by Randy Read). I use .sca from hkl2000 and running program from parameters file. I tried: ... all_plausible_sg_list = True use_all_plausible_sg = True ... all_plausible_sg_list = P222 P2221 P21212 P212121 use_all_plausible_sg = True ... space_group = "P 21 21 21" ... They lead to report that no solution found or program being stalled (last variant). What should I do to make phaser search for all space groups in P222 point group? Thanks, Vitali

3 2

rosetta mr
by Shya Biswas 06 Dec '11

06 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] 06 Dec '11

06 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 04 Dec '11

04 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

pdb hierarchy
by Bradley Hintze 03 Dec '11

03 Dec '11

Hi Phenix, I have a hierarchy question. I was using the hierarchy and got something that I did not expect. when running this: pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy() for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this? Thanks, Bradley

3 2

Writing PDB
by Bradley Hintze 03 Dec '11

03 Dec '11

Hi again, I am trying to take a pdb and write out a new pdb with just a specified chain. I am trying to do this with the hierarchy but am unfamiliar with its functions How do I do this? Thanks, Bradley

3 2

the Ming dial
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, In the Ming dial, there is a occupancy (%), which indication of excellent , good, etc. Does it mean if I choose the "occupancy" of excellent, the rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8, and I find no matter how I turn the dial, the original fits the map best. Currently my rotamer outlier is 8%, thus I need the way to have it solved. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui

2 3

on the rotamer optimization
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, Besides Coot and Ming, is any software or server which could further optimize the side chain outliers? I am looking forward to getting your reply. Cheers, Dialing

1 0

solvent model in phenix.refine
by Weiergräber, Oliver H. 01 Dec '11

01 Dec '11

Hello, the ordered_solvent option in phenix.refine apparently uses these parameters by default: min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds. My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average. On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Clashing alternative conformations
by Sozanne Solmaz 01 Dec '11

01 Dec '11

Dear all, I have the following problem: I have a homodimer of two protein chains A and B, which I refine in Phenix, and one residue has 2 alternate conformations (a and b) for each chain. If the residues of both chains A and B are in the alternative conformation b, they clash. However, I would expect that never both residues are in conformation b, and therefore only the combinations aa, ab and ba of alternative conformations exist. My problem is, that during the refinement, the two b conformations of the residues clash, which drives the clash-score of the overall structure to a very high value and repulsion pushes the two b-conformations apart during refinement, therefore I cannot model them properly. Is it possible in Phenix to define these two conformations as non-clashing and non-repulsive? Thank you, best regards, Sozanne Solmaz.

2 1

"nproc" in phenix.refine
by Jonathan Elegheert 30 Nov '11

30 Nov '11

Dear all, I have a question regarding the "nproc" parameter in phenix.refine; We have the software installed on our university HPC cluster, which has nodes built up of 8 processors each. Submission works via a queuing system ("qsub"). I understand that compiling with OpenMP renders the nproc parameter disfunctional. Does this then imply that I will be limited to 1 node (8 processors) if compiled without OpenMP, since there is no "message passing" to other nodes? Or is there a way to make use of more of the available nodes, for example by compiling with OpenMP and then specifying many nodes with 1 processor? Best regards, Jonathan Elegheert PhD Student Unit for Structural Biology & Biophysics Ghent University jonathan.elegheert(a)ugent.be

2 1

Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
by Yarrow Madrona 29 Nov '11

29 Nov '11

Hello, I am having some trouble refining a structure with Nitric Oxide coordinated to the Heme Fe. I attempted to merge two Cif files. One for another ligand (CNL) and one for NO (NO.cif). I have saved the merged file as CinNO2.cif. In the defualt refinement I type the following into the command line: Mymodel.mtz mymodel.pdb CinNO2.cif Phenix refine runs fine without any errors but pushes the NO much further than the 1.9 angstrom specified by the links in the cif file. I have pasted the contents of the cif file below. The NO, Fe links are at the end of the file. Thank you for any help you can provide. -Yarrow # Files merged : Tue Oct 4 10:11:22 2011 # # CNL.cif # NO.cif # 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 CNL CNL Unknown ligand 29 11 . NO NO Unknown ligand 2 2 . # data_comp_CNL # 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 _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CNL C1 C CT . 55.3085 -9.1280 -43.0216 CNL C2 C CH2 . 55.6432 -10.5699 -43.1750 CNL C3 C CH2 . 54.6509 -11.3139 -43.9725 CNL C4 C CH1 . 53.4902 -10.4784 -44.3504 CNL C5 C CH2 . 53.9278 -9.3349 -45.0693 CNL C6 C CH2 . 54.8932 -8.4964 -44.3064 CNL C7 C CH3 . 56.3801 -8.3679 -42.3275 CNL C8 C CT . 52.9353 -9.9244 -43.0573 CNL C9 C CH3 . 52.3495 -11.0301 -42.2453 CNL C10 C CH3 . 51.8314 -8.9341 -43.2982 CNL O O O2 . 54.1049 -9.2461 -42.2221 # 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 CNL C1 C2 single 1.488 0.020 CNL C1 C6 single 1.491 0.020 CNL C1 C7 single 1.486 0.020 CNL C1 O single 1.450 0.020 CNL C2 C3 single 1.475 0.020 CNL C3 C4 single 1.479 0.020 CNL C4 C5 single 1.420 0.020 CNL C4 C8 single 1.512 0.020 CNL C5 C6 single 1.489 0.020 CNL C8 C9 single 1.492 0.020 CNL C8 C10 single 1.502 0.020 CNL C8 O single 1.589 0.020 # 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 CNL C3 C2 C1 113.16 3.000 CNL C5 C6 C1 112.56 3.000 CNL C8 O C1 110.85 3.000 CNL C6 C1 C2 112.60 3.000 CNL C7 C1 C2 112.43 3.000 CNL O C1 C2 99.48 3.000 CNL C4 C3 C2 112.41 3.000 CNL C5 C4 C3 110.02 3.000 CNL C8 C4 C3 106.05 3.000 CNL C6 C5 C4 113.20 3.000 CNL C9 C8 C4 109.75 3.000 CNL C10 C8 C4 111.96 3.000 CNL O C8 C4 109.61 3.000 CNL C8 C4 C5 104.53 3.000 CNL C7 C1 C6 112.76 3.000 CNL O C1 C6 106.18 3.000 CNL O C1 C7 112.51 3.000 CNL C10 C8 C9 106.70 3.000 CNL O C8 C9 108.62 3.000 CNL O C8 C10 110.10 3.000 # 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 CNL Var_01 C4 C8 O C1 10.40 30.0 3 CNL Var_02 C9 C8 O C1 130.31 30.0 3 CNL Var_03 C10 C8 O C1 -113.19 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 CNL chir_01 C1 C6 C7 O both CNL chir_02 C4 C3 C5 C8 both # data_comp__NO # 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 _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z NO N N N . -5.7690 4.3760 32.3600 NO O O O . -4.8990 5.2460 32.3600 # 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 NO N O double 1.150 0.02 # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name HEM-CYS HEM . . CYS . . bond_CYS-SG_=_HEM-FE NO -HEM HEM . . NO . . bond_HEM-FE_=_NO-N # data_link_HEM-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd HEM-CYS 1 FE 2 SG . 2.300000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000 HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000 # data_link_NO -HEM # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NO -HEM 1 N 2 FE . 1.900000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NO -HEM 2 FE 1 N 1 O 140 3.000 NO -HEM 1 N 2 FE 2 NC 103 3.000 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

4 6

Mn - O distances
by Timothy Springer 29 Nov '11

29 Nov '11

Hi, We are refining structures with Ca binding sites that are replaced by Mn. Using the coordination restraints in Phenix (distance only) obtained with phenix.metal_coordination, we wind up with the ligands coming somewhat too close, so there is positive density on the opposite side of the ligating residue from the metal. We may have a series of problems, including incomplete replacement of Ca by Mn. However, the bigger issue I want to address is coordination number. In the work by Shannon and Prewitt, such as Acta Cryst. B25, 925, metal oxides are examined, and the point is made that the Mn-O distance with a coordination number of 6 is shorter than for 7. Ca commonly has either 6 or 7 ligands, and with 7 ligands (most common) the O cannot squeeze as tightly together and are farther away from Ca. Mn more commonly has 6 ligands, but can have 7. What are the distance restraints in Phenix based on? They seem similar to those in Harding MM, Acta Cryst D62, 678 (2006). This paper lumps measurements for different coordination numbers together for Mn-O and Ca-O distances, but not for Co, Cu, and Zn. It does seem to help to add metal ion restraints in Phenix. Things don't seem to come out as well without them. Would it be helpful to treat 6 and 7-coordinate metals differently? Or should we just loosen the restraints? How does Refmac treat metals? One does not need to add restraints in its case. With my best regards, Tim Timothy A. Springer, Ph.D. Latham Family Professor of Biological Chemistry and Molecular Pharmacology Harvard Medical School http://idi.harvard.edu/springer Immune Disease Institute springer(a)idi.harvard.edu Program in Cellular and Molecular Medicine, Dept. Medicine Div. Hematology Children's Hospital Boston 3 Blackfan Circle, Rm 3103 phone: 617-713-8200 Boston MA 02115 fax: 617-713-8232

4 5

Metal restraints at special position
by Yuri 28 Nov '11

28 Nov '11

I have a Mg2+ coordinated to 4 waters and 2 side chains. Some of the waters are at special postions. I generated the restraints file using "phenix.metal_cordination input.pdb" When I run refine with my .edits restraints file it crashes due to the special position. How do I handle this? Best, -- Yuri Pompeu

2 1

phenix-1.7.2-x refine error
by Christoph Parthier 25 Nov '11

25 Nov '11

Dear Phenix developers, Using the current phenix version, refinements of a 'certain structure' always stop with the error message quoted below, while the refinement of other 'similar structures' work flawlessly. In the error case the three scheduled macrocycles of refinement seem to finish (the refined PDB is there) but at there seems to be problem in finishing the job - the output MTZ file has zero byte length and the last line in refine.log is: ============================== Exporting results ============================== This occurs with several 1.7.2-x versions of phenix, I'm not sure about 1.7.1-x. Interestingly, the 'problem structure' can be refined without problems using the same input files in phenix-1.7-650. Any idea whether this is due to an installation problem or a bug? Thanks, Christoph Here's the error message: MemoryError : Traceback: File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 115, in run map_manger.write_files() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1535, in write_files map_coeff_dataset=self.write_mtz_file(), File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1524, in write_mtz_file params = self.map_params.map_coefficients) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 502, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 353, in map_coefficients_from_fmodel fill_mode = "dfmodel") File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1887, in electron_density_map fill_mode = fill_mode) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/map_tools.py", line 114, in __init__ update_scaling = update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1663, in fill_missing_f_obs fmodel=self, fill_mode=fill_mode, update_scaling=update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 131, in fill_missing_f_obs fmodel = select_by_map_cc(fmodel = fmodel.deep_copy())) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 85, in select_by_map_cc fourier_coefficients = coeffs) File "/cryst/phenix-1.7.2-869/cctbx_project/cctbx/miller/__init__.py", line 3688, in __init__ conjugate_flag=True) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix-1.7.2-869/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Sep 23 2011 __TIME__ = 00:13:14 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.6.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.22.13-GOLIAT-0.3-bigsmp-i686-with-SuSE-10.3-i586 platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 4,238,028,800 Memory free: 3,715,174,400 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Ã

3 3

回复：phenixbb Digest, Vol 72, Issue 10
by dingding830106＠sina.com 24 Nov '11

24 Nov '11

Dear Thomas: I try running phenix.autosol instead of phenix.solve, and it solve this problem. Thanks a lot! Dingwei ----- 原始邮件 ----- 发件人：phenixbb-request(a)phenix-online.org 收件人：phenixbb(a)phenix-online.org 主题：phenixbb Digest, Vol 72, Issue 10 日期：2011年11月23日 01点08分 Message: 14 Date: Tue, 22 Nov 2011 10:08:46 -0700 (MST) From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] solve/resolve problem Message-ID: <52791.128.165.72.7.1321981726.squirrel(a)webmail.lanl.gov> Content-Type: text/plain;charset=iso-8859-1 I'm sorry for the problem! I don't recognize this error (the message solve is giving you is just saying that it has finished, unfortunately). Can you possibly (off-list) send me your input script and the output log file and I'll have a look? Or even better, try running phenix.autosol on the data and perhaps that will solve the problem! All the best, Tom T >> >> >> Dear all >> when I use SOLVE to deal with the SAD data, it will stop with a error >> message: >> >> ???STOP at >> /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)??? >> Can you tell me what happen? >> >> wding >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

1 0

measuring angle
by Hena Dutta 23 Nov '11

23 Nov '11

Hi, Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? I have another question. In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID? As for example:- pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log ROTATE [INVERT] [MATRIX] values CHAIN A end eof This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate. Thank you in advance and have a nice THANKS GIVING WEEKEND Hena

6 8

reference model restrain error
by Stephan Barden 23 Nov '11

23 Nov '11

Dear all, I'm facing a problem with a fresh (yesterday) installation of phenix 1.7.2-869 refining a structure with 6 molecules per ASU at 3.25 A and using a different reference structure with 1 mol/ASU at higher resolution. I wrote an additional parameter file to assign the reference model to each of the six molecules, which worked well with an older version of phenix. After the upgrade neither taking the additional parameter file, nor auto alignment worked for me. The error comming up is always: RuntimeError : Duplicate sequence number and insertion code. Traceback: File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 75, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 209, in __init__ log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 145, in __init__ self.get_reference_dihedral_proxies() File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 611, in get_reference_dihedral_proxies log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 398, in process_reference_groups raise e Has anyone observed a similar problem? Are there any suggestions? Thanks, StephanB.

2 1

solve/resolve problem
by dingding830106＠sina.com 22 Nov '11

22 Nov '11

Dear all when I use SOLVE to deal with the SAD data, it will stop with a error message: “STOP at /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)” Can you tell me what happen? wding

2 1

How to reduce clashscore value
by CelinaSocek 21 Nov '11

21 Nov '11

Hi all, I'm now using phenix to refine a small protein about 300 residues long. The resolution of my data is about 2.9 angstrom. Currently I got a refined model with good R-factors about 23/26, RMSD very reasonable and no Ramanchandran outliers. However, I found that the clashscore is extremely high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind of stretagy I can use to reduce this? Thank you very much! best, Celina

6 16

test_hhr
by Alexander Batyuk 21 Nov '11

21 Nov '11

Dear all, The phenix_regression.wizards.test_command_line_rosetta_quick_tests command hangs at the test_hhr step in phenix-dev-910 on Mac OS X 10.6.8. What could be the reason for that? What kind of log files should I post? The firewall allowed to fetch files from the net. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

2 2

Re: [phenixbb] How to reduce clashscore value
by CelinaSocek 20 Nov '11

20 Nov '11

Thank you Nat! I will try to fix as many clashes as I can in coot, and hope that I can manage to reduce it to around 20. ;) Also thank other suggestions and discussions! best, Celina > > Which version are you using? We made some changes over the summer > that improve the geometry, especially the clashscore - these are > present in version 1.7.2. If you're still using an earlier version, > this might largely fix the problem. However, if there is > conformational strain in the model, it is difficult to fix severe > clashes without further rebuilding. You should inspect the clashes in > Coot (the Phenix GUI has shortcuts for this, but Coot alone also has > this capability) and fix as many as possible yourself. It is > recommended that you use explicit hydrogen atoms when doing this, > since the reason for clashes is often not obvious if only heavy atoms > are used. (You don't necessarily need to refine with heavy atoms > though - they're just an aid to visualizing clashes.) > > The rotamer problem may be related; there isn't much you can do with > these except fix them manually, but relieving some of the clashes may > help. The dihedral angle restraints simply aren't that strong, so in > areas of weak density it can be difficult to completely prevent > outliers. > > -Nat > > > ------------------------------ > >

1 0

multiple ligand conformations
by Leonard Thomas 19 Nov '11

19 Nov '11

Hello All, One of the groups here has run into a problem in the refinement of their structure or more specifically a ligand bound to the structure. Through a series of other experiments they know that a photo reaction occurs to the compound when exposed to high flux as found at your everyday synchrotron source. The exposure changes the bonding such that there are two conformations with a bit in between obviously. They collected 360 degrees worth of data and if the data is split you can model the two conformations depending which half of the data you use. They are trying to refine with all of the data and modeling of the ligand into the two conformations. In refmac they can model this with no problem but in Phenix the ligand adopts a chemically wrong conformation, sort of a halfway point between the two chemically relevant conformations. They have used Phenix to do similar refinements on other structures but it appears either the last release or the latest release is causing problems. They have started out with everything from 50% occupancy to shifting it towards on one conformation or the other and the ligand always ends up in the chemically wrong position. Data is in the 1.4-1.5 ang. range. Ideas? Thanks in advance. Len Leonard Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 lmthomas(a)ou.edu http://barlywine.chem.ou.edu Office: (405)325-1126 Lab: (405)325-7571

2 1

multiple ligand conformations
by Yuri 19 Nov '11

19 Nov '11

Hi, When you say "wrong postion", what does it mean? are the 2 ligands you are trying to refine being "pushed away" from each other? If that is the case first thing I would check is the ALTLOC comlumn of their pdb file entries. Make sure one is ALTLOC A and the other ALTLOC B. I have refined with ligands in four different positions before using phenix before and got satisfactory results... Hope this helps, -- Yuri Pompeu

1 0

MR_ROSETTA
by Wei Shi 18 Nov '11

18 Nov '11

Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

7 9

error: Duplicate selections
by Sebastiano Pasqualato 16 Nov '11

16 Nov '11

Hi all, sorry guys, this might be a silly one, but I can't see where I'm making the mistake. Whenever I turn on TLS refinement, I get this error message. And, as you can see, the Log file doesn't tell me much more. I have generated the TLS groups wit the 'TLS groups selection' tool in phenix. Any hint? Thanks in advance, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

2 2

Scattering from riding hydrogens?
by Damian Ekiert 15 Nov '11

15 Nov '11

Hello, I have a question regarding two parameters and how they affect riding hydrogens. contribute_to_f_calc = True high_resolution_limit_to_include_scattering_from_h = 1.6 At lower resolution, setting contribute_to_f_calc = false is frequently helpful when using riding hydrogens and has been discussed before. But what is high_resolution_limit_to_include_scattering_from_h = 1.6 doing? If scattering from hydrogens is only included at higher than 1.6A resolution, it would seem like contribute_to_f_calc = True/False would not have any effect at say, 3.5A, but comparing identical refinement runs with contribute_to_f_calc = True or contribute_to_f_calc = False clearly gives different results. Can hydrogens contribute to Fcalc in a way aside from their scattering, or is their contribution accounted for independent of the position of the riding hydrogen (e.g., additional scattering term added to the associated heavy atom)? I think I am misunderstanding what these two parameters are doing and would appreciate some clarification. Thanks, Damian Ekiert

4 5