- phenixbb - phenix-online.org

ensemble refinement rfree values
by Arjun Raman 19 Dec '13

19 Dec '13

Dear Phenix Guys, I have recently been trying my hand at the ensemble refinement option in phenix.refine. I generally observe an increase in rfree after performing the ensemble refinement with a well refined (using anisotropic B) structure, but the r-free increases are fairly small. For instance, 18.53% to 18.9% (1.8 Angstrom structure) or 20.45% to 21.1% (1.9 A)...I understand what this technically means (the ensemble refined model isn't as good) but given the noise in the calculation due to the limited number of reflections for the test set (~1000), would someone consider these rfree increases significant? My apologies if this question is a well-answered one...I can't seem to find much discussion about the range of rfrees to be expected or whether a 0.3-0.5% increase is large enough to toss out the refinement. Normally, I would take the lower rfree but because the ensemble refinement procedure gives potentially much more information, this seemed like a relevant question to ask. Thanks so much for your time, Arjun Raman Ranganathan Lab UT Southwestern ________________________________ UT Southwestern Medical Center The future of medicine, today.

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MR-SAD, Yb, combined phases
by Joseph Noel 19 Dec '13

19 Dec '13

Hi All, I am carrying out a structure refinement using experimental phases combined with an MR solution. The experimental phases are being determined from bound Yb3+ cations and the data is collected at one of the Yb absorption peaks of 1.385 A. I do have a few questions about the heavy atom arrangement and then refinement. At this wavelength, I am also seeing peaks after running MR-SAD that are actually not the Yb cations but the sulfurs on several of the proteins Cys and Met residues. Should I try and change this "heavy atom arrangement" to include Yb and S before determining the final refined phases that I would like to then use as restraints during the structure refinement? If so, its not clear how to do this in Phenix without it finding additional sites that it attributes to Yb but which are actually sulfurs. For MR, this is an exact structure. All I am doing is using Yb which substitute for Mg coordination sites as a source of experimental phases to see how it improves refinement and maps. Second, when I do refine using the MLHL target function, I am finding quite a bit of excess positive density around the Yb sites. How do I try and account for this? I have attempted to take care of it with ADP and occupancy refinement but that doesn't seem to be enough. The resolution is 2.2 A and the anomalous signal is quite good (alas that is why I am also seeing the sulfurs clearly in the anomalous difference map). Do I need to change the scattering table since the structure now includes at least 4 Yb cations per asymmetric unit (one 550 amino acid residue protein per asymmetric unit - 68% solvent)? Is it important to refine the anomalous groups? For the latter, one can't refine with phase restraints (MLHL) and anomalous groups together. I have to choose one or the other - no phase restraints and anomalous groups refined, or experimental phase restraints and no anomalous group refinement. My goal is to use additional experimental measurements - amplitudes and phases to improve refinement, map interpretation and ultimately ensemble refinement. Any help, comments, criticisms, etc will be very appreciated! Happy Holidays! Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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phenix.rosetta_refine on OS X?
by Ben Eisenbraun 19 Dec '13

19 Dec '13

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Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 16 Dec '13

16 Dec '13

We are offering RapiData 2014, the sixteenth 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 27 April - 2 May 2013: 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. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 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 an 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 (no more than 30 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 yourself, 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/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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off topic - linux flavors for crystallography
by Todd Jason Green 12 Dec '13

12 Dec '13

Hello All- I have used a trusty box running fedora core 3 for nearly a decade and I am (finally) upgrading to a new workstation. In lieu of Nat's recent mention of new linux installers of phenix, I thought I would try to get a consensus on what linux flavor(s), I should consider installing on my new box. It will be used with emphasis on typical crystallography software including 3D graphics (3 GB NVIDIA Quadro K4000 card). If anyone would like to make a suggestion for an OS, I thank you in advance. Pointers to a web review can work too. Best- Todd

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cyclic peptide refinement
by wei xia 12 Dec '13

12 Dec '13

Hi, I am trying to refine a structure with a cyclic peptide ligand.I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.But there is obvious no bond formed between the two residues in the refined structure.I checked the geo file and found that there are only angle restraints but no bond restraints between the two residuesAnyone can help me out?Thanks in advance! Wei P.S. refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain D and resname MVA and resid 5005 residue_selection_2 = chain D and resname ARG and resid 5001 }

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phenix.find_ncs_from_density density_search.dump_ncs_density doesn't output mtz
by Francis Reyes 11 Dec '13

11 Dec '13

I'd like to see the region of my maps that obey the NCS operators and I was hoping for separate mtz's for each region given I had set density_search.dump_ncs_density = True. However, I'm not getting any output mtzs. Any ideas? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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phenix.refine nproc
by de Waal, Parker 10 Dec '13

10 Dec '13

Hello Everyone, I recently compiled phenix 1.8.4-1496 on a CentOS 6.4 server and am having trouble using phenix.refine in parallel using the nproc flag which always runs as a single thread. Please find my input parameters here: https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a I'm wondering if maybe OpenMP isn't configured properly on our server? Or maybe the correct version is not installed when I compliled phenix. If anyone has any input or experience with a problem such as this I would be extremely grateful. Cheers, Parker

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Spatial filtering
by Machius, Mischa Christian 06 Dec '13

06 Dec '13

Potentially silly question: is spatial filtering used for increasing contrast in electron density maps? Is it used for any other kind of data manipulation in macromolecular crystallography, e.g., diffraction data processing, density modification, etc. I'm a bit fuzzy on that subject, and so I said 'potentially silly', because it could be that such approaches are totally common but have different names (such as local averaging/scaling and so on). Many thanks in advance. Cheers, MM

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Submissions for next CCN newsletter
by Nigel Moriarty 06 Dec '13

06 Dec '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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