December 2011 - phenixbb - phenix-online.org

AutoBuild Question
by Page, Rebecca 13 Dec '11

13 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

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phenix.refine_failed
by Xue-Yuan Pei 13 Dec '11

13 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 >

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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

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Phaser not writting out ligands
by Yarrow Madrona 10 Dec '11

10 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

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Please apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 10 Dec '11

10 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) =========================================================================

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map output from ncs_average
by Ursula Schulze-Gahmen 10 Dec '11

10 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

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print_sequence
by Bradley Hintze 10 Dec '11

10 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

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excluding atoms from refinement
by Crystal VanderZanden 09 Dec '11

09 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

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Re: [phenixbb] Autosol problems
by Tom Terwilliger 09 Dec '11

09 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

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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

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