- phenixbb - phenix-online.org

modelling a flexible peptide
by intekhab alam 04 Apr '12

04 Apr '12

Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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fwd: Application deadline approaching: CCP4 summer school at APS, in USA
by Nathaniel Echols 03 Apr '12

03 Apr '12

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Cc: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> Date: Tue, 3 Apr 2012 17:19:36 -0500 Subject: Application deadline approaching: CCP4 summer school at APS, in USA Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world’s leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Trueblood Award Nominations
by Paul Adams 03 Apr '12

03 Apr '12

Dear Colleagues, on behalf of the selection committee I'd like to draw your attention to the the Trueblood award: http://www.amercrystalassn.org/content/pages/main-award-descriptions This will next be awarded in 2013, however nominations are sought now so that the winner can be announcement this Summer. The award will be presented at the 2013 ACA meeting. Please follow this link to obtain the nomination form: http://www.amercrystalassn.org/documents/ACAnomNEW.pdf Note that the deadline for nominations is May 1st, which should be sent to marcia(a)hwi.buffalo.edu. Here is a summary of the award: Kenneth N. Trueblood Award To recognize exceptional achievement in computational or chemical crystallography. The award is established in memory of Professor Kenneth N. Trueblood, UCLA 1949-1998, who was a major force in the early use of computers and the development of crystallographic computer programs. He applied these programs to the examination of chemical and molecular details of many structures at the frontiers of research. His contribution to the famous work on vitamin B12 is one example. Professor Trueblood was a leader in the development of techniques for analysis of anisotropic motion and was also a superb teacher and a lucid author. Established in 2001, the award will be given every three years and consist of an honorarium of $1,500 and up to $1,500 in travel expenses to accept the award. -- 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 ] --

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Exhaustive List of Phenix Commands
by Matthew J. Whitley 03 Apr '12

03 Apr '12

Hello all, I was wondering if somewhere, either on the web or in hardcopy, there is an exhaustive or nearly exhaustive list of Phenix commands. For example, from a Phenix BB thread earlier in the day I learned of the existence of the phenix.r_factor_statistics command for gaining insight into where your R/Rfree values place you in regard to structures of similar resolution. As I read more of the messages posted to the Phenix BB, I become aware of more and more nifty things that Phenix can do that I simply was not aware of, and I was wondering if some kind of master list of Phenix commands is available somewhere. Thanks to all the developers for making this amazing program available to the x-ray community. 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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amazing good statistics add
by Christian Roth 03 Apr '12

03 Apr '12

In general the Rvalues of course fit very well Rmerge. A good sign that it should be fine, as far as I remember correctly about the theoretical limits for the Rvalues after refinement compared to the experiment. Best Regards Christian

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Creating dictionary restraints for a LINK
by Mario Sanches 03 Apr '12

03 Apr '12

I have a question regarding link dictionary generation. Nigel helped me with a molecule dictionary last week (thank you Nigel) so the molecule is refining well now. This molecule is covalently bound to on of the residues. I tried generating a dictionary that describes both the molecule and the link but so far phenix.refine is ignoring it. Again, the molecule itself refines very well but the link is not there. What is the best way to define it? Thank you very much. -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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DEN refinement is crashing
by Mario Sanches 02 Apr '12

02 Apr '12

I am running phenix.refine using the graphical interface. Under "global refinement paramerters..." I am selecting "DEN". The problem is that Python crashes all the time, always at the same point (see portion of the log output below). Is it a known bug? Is DEN incompatible with some of the options in refinement? My resolution is 2.9A by the way. Thank you for your inputs. Mario Sanches ___________________________ Log output final portion: tardy dynamics: number of bodies: 3678 number of degrees of freedom: 3713 number of atoms * 3: 38220 ratio: 0.097 = 1/10.29 temperature degrees of freedom: cartesian (38220) kinetic energy sensitivity to generalized velocities: n: 3713 min: 3.61771e-06 max: 0.0300001 mean: 0.00410663 time step: 0.00100 pico seconds velocity scaling: True suppressing allowed origin shifts: False new target temperature: 2500.00 K step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214 -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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labelit.index is too precise not to allow 0.000001 deg difference
by fukamitka＠chugai-pharm.co.jp 02 Apr '12

02 Apr '12

Dear Phenix developers, I had a problem in indexing by labelit.index in phenix-1.7.3-928, getting the error below: InputFileError: Input error: All images must have same oscillation range (delta phi). My dataset was collected by inhouse R-axis with 0.8 deg oscillation. Image header values of oscillation range fluctuate between 0.799999 - 0.800004 degrees. When I specified two images whose delta phi angles were different, say 0.799999 and 0.800003, labelit.index stopped with the error above. I don't think a goniometer have such a precision, therefore I think line 249 in /phenix-1.7.3-928/labelit/command_line/imagefiles.py should be modified not to use == instead of similar_delta_phi() or something. 246 if False in [similar_wavelength(self.images[0],self.images[x]) for x in xrange(1,Nimages)]: 247 raise InputFileError("""All images must have similar wavelength.""") 248 249 if False in [self.images[0].deltaphi==self.images[x].deltaphi for x in xrange(1,Nimages)]: 250 raise InputFileError("""All images must have same oscillation range (delta phi).""") Best regards, Takaaki Fukami ----- Dr. Takaaki Fukami (mailto:[email protected]) Discovery Research Dept. (Biostructure Gr.) Roche Group: Chugai Pharmaceutical Co.,Ltd.

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very informative - Trends in Data Fabrication
by Bosch, Juergen 31 Mar '12

31 Mar '12

really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421> Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.> Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/

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Problems fitting NADH
by Phillip Steindel 30 Mar '12

30 Mar '12

Dear all, I'm trying to fit a NADH into a 1.7 Å structure. LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly). I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated. Thank you, Phillip Steindel Theobald Lab Department of Biochemistry Brandeis University

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