February 2012 - phenixbb - phenix-online.org

(no subject)
by intekhab alam 10 Feb '12

10 Feb '12

Hi all I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given peptide: MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLE 1.Based on map features which segemnt should i start with. 2. Is there anyway that i can build the best fit segment of my second protein. I tried autobuild but it failed to build any peptide for my second protein. Your help is highly appreciated. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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phenix.ready_set
by Jianghai Zhu 10 Feb '12

10 Feb '12

Hi, I am using phenix.ready_set (version 1.7.3) to add hydrogens to my structure. I found out that it makes a few mistakes when dealing with glycans. It adds hydrogens to C1, O4, O3, O6 even when these atoms have formed covalent bonds with other sugars and residues. Subsequent phenix.refine aborts because of these incorrect hydrogens. However, when I use phenix.reduce directly, all hydrogens are placed correctly. I assume something went wrong in phenix.ready_set. The problem with phenix.reduce is that it doesn't know how to deal with ligand whereas phenix.ready_set does when a cif file is provided. -- Jianghai

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sa_omit map calculation
by Ursula Schulze-Gahmen 08 Feb '12

08 Feb '12

I want to calculate a sa-omit map around the same small region in the 3 molecules in the au. I have 2 questions: Can I include the 3 regions in the same omit box file? What does the following advice in the manual mean: (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). I am not sure what weights we are talking about? Thanks for any help. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Assigned occupancy refinement
by Fischer 08 Feb '12

08 Feb '12

Hello PhenixBB, We are interested in refining 3 distinct backbone conformations of a loop (A, B, C). Our crystals are very high resolution and the density is fairly distinct for each of these conformations. In the simplest case - each individual backbone conformation has one residue in two alternative side chain conformations. (A1,A2; B1,B2; C1,C2). We'd like to keep each pair of conformations assigned to the respective loop and then refine all six occupancies. Is there such an option similar to the free parameters in shelx also available in phenix? Thanks, Marcus

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Rosetta Fragment viewer
by 商元 08 Feb '12

08 Feb '12

Dear all, Is there any program that can view the fragment files generated from Rosetta Fragment library? For example, I want to build a model myself, and I know the secondary structure of the target protein, so I will dock the 9-fragment myself. But, at the first step, I have to choose one fragment from the Rosetta fragment library generated. So, I wish if I can find any program that integrate the 200 9ers at specific position together, and then choose a good model by the shape I wanted. Did anyone here know such a program? Best Regards, Yuan SHANG

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phenix.table_one
by Hasan Demirci 08 Feb '12

08 Feb '12

Hi, I am running phenix-dev-978 (fedora core 15 installer) version on a quad core intel chip computer. How can I obtain a table without digging a lot of files? When I use command line and try to run phenix.table_one I am getting the following AssertionError message: Is it a mistake in the input files or is it a bug in this version of phenix I am using? Thanks. ------------------------------------------------------------------------------- phenix.table_one f71c_refine_006.pdb outputf71c.mtz note: this is somewhat difficult to configure on the command line at present; you may find it more convenient to use the PHENIX GUI. Attempting to guess labels for outputf71c.mtz... Attempting to guess R-free label for outputf71c.mtz... #Final effective parameters: table_one { structure { name = None pdb_file = "f71c_refine_006.pdb" mtz_file = "outputf71c.mtz" data_labels = "IMEAN_wt30Sapo,SIGIMEAN_wt30Sapo" r_free_flags.label = "FREE" log_file = None cif_file = None cif_directory = None data_type = *xray neutron } processing { parallel = False re_compute_r_factors = False } multiprocessing { enable_multiprocessing = True method = *mp sge nproc = 1 tmp_dir = None } output { directory = "/home/Demircha/Desktop/test" job_title = None show_missing_fields = True format = *txt csv *rtf base_name = "Table1" verbose = "True" text_field_separation = 2 } } #---end Running phenix.model_vs_data for all structures. . . Multiple segs ' ' 12 'A ' 12 Use --do-all to process all residues not in internal library Traceback (most recent call last): File "/xsoft/phenix-dev-978/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 7, in <module> use_current_directory_if_not_specified=True) File "/xsoft/phenix-dev-978/phenix/phenix/automation/table_one.py", line 424, in run out=out).collected_stats File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 173, in __init__ results.append(run_model_vs_data(structure)) File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 93, in run_model_vs_data log=null_out()) File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/model_vs_data.py", line 744, in run mmtbx_pdb_file.set_ppf(stop_if_duplicate_labels = False) File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/utils.py", line 1819, in set_ppf silent=True, File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2310, in run model_vs_data=model_vs_data, File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 732, in elbow_on_pdb_file molecule = extract_polymer_unit(pdb_inp, molecule, code) File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 213, in extract_polymer_unit if residue_group.resseq.strip() == molecule.GetSequenceID().strip(): continue File "/xsoft/phenix-dev-978/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 1575, in GetSequenceID assert 0 AssertionError

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Composite Omit Map Calculations - Batch Que
by Matthew J. Whitley 07 Feb '12

07 Feb '12

Hello all, I usually set up simulated annealing composite omit map calculations via the Phenix GUI and set the number of processors equal to 2 to take advantage of my Mac's dual core processor in order to shorten the calculation time somewhat. My department does have a high performance cluster, however, and I would like to start using that multi-node system to shorten the calculation time substantially. The problem for me is that the high performance cluster requires jobs to be submitted and managed via a PBS queue. I know how to specify in the PBS shell script the computing resources I want to use (say, for example, 8 dual core processors for a total of 16 nodes). My question is, do I need to specify any additional settings in the actual Phenix command line execution statement? For example, nproc = 16? Anything else? The entire shell script containing the PBS setup statements and the actual Phenix execution statements is submitted by the qsub command. In essence, I am wondering how to get Phenix to "play nicely" with the queueing system such that the composite omit calculations will be distributed box by box over the resources I reserve via the PBS statements. Thanks in advance for any advice. Also, if anybody has experience running Phenix jobs via a shell script submitted to a batch queueing system, I would very much appreciate the chance to look at the shell script. Thanks, Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine

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Difference in water molecules count
by bsubedi＠btk.fi 07 Feb '12

07 Feb '12

Hi All, I have been refining the mutant structures and at the end while making the comparative study I found that there is a large difference (almost half) number of water molecules in the protein strucutre of same mutant from different crystal conditions. The resolution of the structure, space group and no.of molecules in a.s.u is same. Here is the data collection statistics and no.of water & protein atoms present. I could also not understand the difference of unique and measured reflections at same resolution. Could anyone please explain me? Resolution range (Å) 20-1.6 (1.64-1.60) 20-1.8 (1.85-1.80) 20-1.9 (1.99-1.94) 20-1.6 (1.63-1.59) 20-1.6 (1.64-1.60) Number of measured reflections 221864 (14118) 173933 (9556) 85976 (5129) 206723 (12667) 262291 (15803) Unique reflections 84896 (6139) 59955 (4010) 38628 (2777) 86161 (5992) 85305 (5803) Completeness (%) 98.7 (97.2) 95.9 (87.9) 77.6 (75.5) 93.9 (87.9) 97.8 (90.9) No of protein atoms 5101 5096 5076 5113 5120 No of waters 1103 528 453 585 1214 Thanx, World

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CASP Roll: Call for novel fold and membrane protein targets to help improve structure modeling methods
by Torsten Schwede 06 Feb '12

06 Feb '12

Dear colleagues, As many of you know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. The regular CASP experiments collect target information for a three month season every two years, and in that period, thanks especially to the structural genomics community, can acquire over 100 targets, sufficient to evaluate the state of the art for most types of template based modeling. There are some classes of target, specifically proteins with novel folds and membrane proteins, where there are not enough structures solved in three months to provide sufficient information so the methods can be fully evaluated. As a consequence, progress is slowed. To address this problem, with the encouragement of the modeling community, CASP has launched a rolling mechanism, where we accept targets in these categories at any time. Of course for that to work we rely on you, the experimentalists, to provide suitable targets! So we are asking that you tell us about structures in these categories that are about to be solved whenever they come up. For those of you who have not provided targets to CASP before, the procedure is simple – there is a web page for submitting targets, and a very experienced staff to deal with any queries. We don’t need the structure in advance of its release by the PDB, and if we are notified early enough (a minimum of three weeks before release, more is better) there need be no delay in structure release. If you have a suitable target now, we are up and running with 50+ prediction teams already submitting models, and would love to have your targets. Most important, the modeling community is now in continuous need of your assistance, so please get in touch whenever an opportunity arises in the future, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, University of Basel & SIB, Switzerland Anna Tramontano, University of Rome, Italy Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casprol/ CASP Roll targets so far: http://www.predictioncenter.org/casprol/targetlist.cgi Submit a target: http://www.predictioncenter.org/casprol/targets_submission.cgi 1. Critical assessment of methods of protein structure prediction (CASP)--round IX. Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14. 2. CASP9 results compared to those of previous CASP experiments. Kryshtafovych A, Fidelis K, Moult J. Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 Oct 14.

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FW: Summer Internship at Merck for Ph.D. students
by Soisson, Stephen M 06 Feb '12

06 Feb '12

All, We have a summer internship opening at Merck (see below for the details) for graduate students in the Global Structural Chemistry/X-ray crystallography/Biomolecular NMR group at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 10-12 weeks. If you are interested please visit our career site at www.merck.com/careers<http://www.merck.com/careers> to create a profile and submit your resume for requisition #CHE003379. Sincerely, Steve Soisson -------------- Job Description X-ray Crystallography/BioNMR Summer Internship 2012 - PhD:CHE003379 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. Merck Research Labs will be offering 2012 summer internships in the Global Structural Chemistry group (X-ray crystallography or Biomolecular NMR) at either its Kenilworth, NJ or West Point, PA sites. Internships will begin in early June 2012, and will run for 9-11 weeks. A suitable candidate has a science background with interest in the use of X-ray crystallography and/or Biomolecular NMR in drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. Candidates will gain firsthand experience in modern drug discovery, and will also make valuable contacts within the industry. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications Required: * Currently pursuing a Ph.D. in Biomolecular NMR, X-ray crystallography, Computational Chemistry, Biophysics or a related field * Applicants must be available for full-time employment for 9 - 11 weeks during the months of June - August 2012. Preferred: * Experience in one or more of the areas of protein crystallization, X-ray theory, X-ray crystallography or Biomolecular NMR * Strong math and/or physical science background with expertise in computers and computer programming * Science background with an interest in computers and drug discovery Our employees are the key to our company's success. We demonstrate our commitment to our employees by offering a competitive and valuable rewards program. Merck's benefits are designed to support the wide range of goals, needs and lifestyles of our employees, and many of the people that matter the most in their lives. To be considered for this position, please visit our career site at www.merck.com/careers<http://www.merck.com/careers> to create a profile and submit your resume for requisition #CHE003379. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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