- phenixbb - phenix-online.org

phenix.refine and multi-metals centers
by Carlos Frazao 09 Mar '10

09 Mar '10

Hi I have a doubt on the refinement of e doubled metal center. I know that: 1) one may fix the metals to their actual positions by using e.g. refine.sites.individual="not element Fe" 2) one may use "phenix.metal_coordination my.pdb" to obtain a dictionary for the actual metals coordinations but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ? Thanks a lot, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX: (351)-214433644 e-mail: frazao(a)itqb.unl.pt www.itqb.unl.pt

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molprobity todo list and coot integration in linux
by hari jayaram 09 Mar '10

09 Mar '10

Hi, Is a difference in the way the GUI molprobity TODO list is displayed between linux and Mac OSX . I am running 1.6.289 on both ...and have coot with scheme and python scripting installed, On mac OSX , phenix starts up coot with the molecule and maps loaded after a phenix.validate and a TO-DO list in a separate GUI window In Linux these separate To-do list windows dont seem to open . ..I have looked everywhere and the dont seem burried behind something else, Is there some setting I need to toggle to have these popup , sortable todo lists for molprobity assisted rebuilding on Linux systems? Thanks for your help Hari

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Autosol + MR
by Manoj saxena 07 Mar '10

07 Mar '10

Hi, I have partial solution from MR on a crystal with dimensions 52.729 60.364 142.908 90.00 90.00 90.00 P 21 21 21. I have SAD data from another crystal with dimension 53.860 61.470 142.492 90.00 90.00 90.00 P 21 21 21. My question is can I treat both as isomorphous and combine data from both of them and use my MR as model with Autosol. What is the maximum difference in unit cell dimensions allowed to consider two unit cell isomorphous? If you can point to some references/examples that will be highly appreciated. Thanks a lot. Marusa

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phenix.reduce segmentation fault with -trim option on Snow leopard Mac OSX
by hari jayaram 05 Mar '10

05 Mar '10

Hi I am running the phenix.reduce with the -trim option and getting a segmentation fault with phenix version 1.6.289 I will remove the molprobity introduced hydrogens using pdbtools ..but thought I will write in with this Thanks Hari $ phenix.reduce s3-3_2.1_refmac0-coot-15_refmac0FH.pdb -trim > s3-3_2.1_refmac0-coot-15_refmac0FnoH.pdb reduce: version 3.15 11/6/2009, Copyright 1997-2009, J. Michael Word Processing file: "s3-3_2.1_refmac0-coot-15_refmac0FH.pdb" Segmentation fault

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coot integration require coot with python?
by hari jayaram 04 Mar '10

04 Mar '10

Hi Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run. Any ideas on how to have them talking to each other? Thanks Hari

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autosol and NCS
by hli＠uci.edu 04 Mar '10

04 Mar '10

I have solved a structure by MR with Phaser. There are 4 copies of molecules per ASU. Parts of the search model are not agreeable with the new structure leading to messy density in some regions. Now a set of SAD data has been collected. I want to run Autosol (MRSAD) to combine the SAD and model phases, doing density modification including the NCS. Can I run simple_ncs_from_pdb to get the NCS operators from the MR solution pdb file and use them for Autosol? Thanks for help. Huiying UC Irvine

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Phaser phasing power statistics
by Daqi Tu 03 Mar '10

03 Mar '10

Hi, I was trying to find phasing power statistics from phenix.autosol log file but couldn't. My structure was phased by Phaser SAD module in phenix.autosol, all I could find was figure of merit. I then ran Phaser SAD within CCP4 and still could not find phasing power statistics from its log. Does anyone know if Phaser SAD generates phasing power statistics in its log file at all? Thanks. Daqi Tu Postdoc Eck lab Harvard medical school

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SAD + Xray = ???
by J. Fleming 02 Mar '10

02 Mar '10

Hi, I have a set of Se-Met SAD data, high resolution x-ray data, and a protein sequence. Is there a way to combine these data sets in Phenix and carry out an autobuild? I saw a section in the manual about MRSAD but that requires a starting model. I've used the SAD data alone to generate a model but I'd like to use both data sets together. Thanks for your thoughts, -Jon

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ICCBM13 - Call for abstracts now open!
by Valerie Pye 02 Mar '10

02 Mar '10

Apologies for this being off topic - but may be of general interest: * * * * *13th International Conference on the Crystallisation of Biological Macromolecules* Trinity College Dublin, Ireland 12th – 16th September 2010 *Crystallization Workshop* – 9th – 12th September 2010 Call for Abstracts Now Open <http://www.iccbm13.ie/abstracts.html> The *13th International Conference on the Crystallisation of Biological Macromolecules* (*ICCBM13 <http://www.iccbm13.ie/>*) is the meeting of choice to learn about the latest research and developments in biomacromolecular crystallogenesis for structure-function-rational design applications. At ICCBM13 leading academic and pharmaceutical scientists will report on challenging systems to include macromolecular complexes and membrane proteins with an emphasis on novel practical as well as mechanistic aspects of crystallogenesis. To cater to the needs of the individual wanting to learn how to grow crystals or to acquire new crystallisation skills, the Conference is preceded by a *Workshop <http://www.iccbm13.ie/workshop.html>* devoted to hands-on instruction on select aspects of macromolecule production and crystal growth. The Conference will be held at *Trinity College Dublin <http://www.tcd.ie/>, Ireland* from the 12th to the 16th September 2010. Convenient and affordable housing is available on and around Trinity College. The campus is situated in the heart of Ireland’s capital city and is surrounded by a diversity of restaurants, pubs, theatres and other points of interests. *Scholarships <http://www.iccbm13.ie/scholarships.html>* are available to Graduate Students and Postdoctoral Fellows. Additional information is available at *www.iccbm13.ie* *ICCBM13 Congress Secretariat* T: + 353 (0) 1 400 3626 F: + 353 (0) 1 400 3692 E: info(a)iccbm13.ie W: www.iccbm13.ie *C/O Keynote PCO* Suite 26, Anglesea House, Blackrock Co. Dublin, Ireland www.keynotepco.ie

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twin refinement
by subhash bihani 02 Mar '10

02 Mar '10

Hi i am refining a protein strucutre with space group P61. Intesity statistics doesnot suggest any twining but refmac and phenix xtriage suggest a twin operator with fraction 0.48. when refined with this twin operator R factors come dowm by 3-5% and also map looks much better. but upon closer inspceion it seems that maps are heavily biased toward the model in both refmac and phenix ( I have mutated one lysine to his and it changed the map to cover his). my question is why twin refinement maps are biased and what are the ways to overcome this. my second question is how to decide whether to use twin refinement or not. is it depends on R factor statistics or we have to check some other parameters. thanks in advance subhash bihani scientific officer Bhabha Atomic Research Centre Trombay-400085 Mumbai(M.S.) India Ph. +912594688 (o) +919322191020 -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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