- phenixbb - phenix-online.org

help with validating a very low res structure
by Yunji Wu 14 Apr '12

14 Apr '12

Hi there-- Any old school experimental phasing experts want to help me out? I have an 8 angstrom structure solved using molecular replacement, refined to Rwork 0.38 and Rfree of 0.47. I also have a heavy atom (not SeMet) derivative data set to 10 angstroms. The idea is to get as much information from these data as possible so as to validate my current MR model. My approach is to calculate a difference map using the isomorphous difference Fouriers OR anomalous difference Fouriers as the amplitudes, with phases derived from the MR model-- then using the difference map to locate putative heavy atom sites. I would use various controls and experiments to (computationally) validate the credibility of these sites (e.g. cross-phasing with only iso/ano differences). Anyone have any suggestions for how to do this using Phenix? I use the GUI (generally the nightly builds), and am a newcomer to Phenix. Thanks!!

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Re: [phenixbb] on the protonation state of HIS
by Ho Leung Ng 14 Apr '12

14 Apr '12

Hi Dialing, What resolution is your structure? We are developing a method to predict hydrogen atom positions from structures of more modest resolution (out to about 1.7 A). We'd be happy to take a look at the histidines in your structure. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

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Windows installer now available
by Paul Adams 13 Apr '12

13 Apr '12

Dear Colleagues, as a result of some very hard work by several members of the Phenix Team, especially Nat Echols, I'm happy to report that we now have an experimental Windows installer for Phenix available for testing in the latest nightly builds. This includes most of the Phenix components, including the GUI, and should run on Windows XP or newer. Coot and PyMOL integration is supported if these are installed. Details are available here: http://www.phenix-online.org/platforms/windows.html We encourage anyone using this to submit the automatic bug reports, or email us concerning any other problems at bugs(a)phenix-online.org. An official, fully supported Windows installer, including 64-bit version, will be available later this year. The Phenix Team -- 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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amazing good statistics
by Christian Roth 11 Apr '12

11 Apr '12

Dear Phenix people, is there a major improvement in the algorithm? I have refined a 2.2 Ang. room temperature dataset with very good data statistics (I think) Rmerge 3.7%(8.9%) completeness 96%(92%) I/sigI 16,6(8,8) in parentheses are the values for the highest resolution shell. After refinement I have a R/Rfree of 0.1294/0.1670. In some shells there are values close to 0.100 and in the lowest shell Rfree is lower than Rwork. The quality of the data are really quite good, what is probably one of the reasons, but I am close or below to the border of the Range of R values in the pdb. Great for me, but I wanna be sure that it is really true. It was a MolRep with a close homolog, but I run a torsion angle sim annealing to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent too much model bias. Best Regards Christian

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Unrestrained refinement and reported RMSD values
by Yuri 10 Apr '12

10 Apr '12

Hi all, I wonder if there is a way of turning off (loosening) restraints for certain residues and a ligand specifically, and will the bond/angle rmsd be printed out somewhere? Thanks -- Yuri Pompeu

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Limit Ramachandran restrain to certain region
by Nian Huang 04 Apr '12

04 Apr '12

Dear all, Is it possible to limit Ramachandran restrain to specified residues in phenix.refine? I have a couple of loops with very poor density. The refinement process always made some residues fall out of ramachandran plot no matter how I tightened the weight and adjusted the residues back. Because the diffraction is about 2.3 A, I don't want the ramachandran restrain to impact the rest of structure. Thanks. Nian Huang

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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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