- phenixbb - phenix-online.org

a small trick for SDS-Gel storage
by Kevin Jin 21 Mar '12

21 Mar '12

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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A possible conjugative relaxase with novel fold for DNA cleavage?
by Kevin Jin 20 Mar '12

20 Mar '12

Dear All, The protein structure of Jann_2411 (PDB 3H0N) from Jannaschia sp. strain CCS1 carries a novel fold for unknown function. Zn-finger is indentified in the C-terminus. However, the N-terminus with a metal binding site presents a novel fold. As the person who solved and characterized this protein, I would like to put some further observation here for your consideration. My analysis is available here: http://www.jinkai.org/Novel_fold_3H0N.html Best regards, Kevin -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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NCS operators
by Melania Strycharska 20 Mar '12

20 Mar '12

Dear all, I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes. I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators. Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry? Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A) Can I choose to apply NCS symmetry to just my backbone? How would I specify that? thanks so much! Melania

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GUI parameter files
by Leonid Sazanov 19 Mar '12

19 Mar '12

Hi, I have a following problem in dev-874 version: If I restore a previous job in refine GUI, to run it with modified settings, and include a new parameter file .eff with definitinon of secondary structure restrains, these new restrains are combined with previously used restrains. How do i get rid of previous restrains? Older file is not visible in inputs, but its settings are still used. And in general, how can one be sure which parameters are used at the start of each refine run? If older settings loaded from .eff or .param file are not visible, the only way is to look through new .eff file, which takes a lot of time. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Refinement using data with pseudo translational symmetry
by Bret Wallace 18 Mar '12

18 Mar '12

To all, First I apologize for the long email, but I wont to make sure that I give enough information to describe the problem. I have been working on a structure of two proteins in complex with each other (one forms a homodimer, with each monomer bound to 1 monomer of the other protein), using data, that according to phenix.xtriage contains pseudo translational symmetry (output pasted below). I have done a lot of searching of both the phenixBB and ccp4BB regarding solutions to this problem, but unfortunately most responses seem to be directed at resolving issues with MR. I have successfully performed MR using both phenix phaser, ccp4 phaser (the most updated version), as well as molrep. The issue arises upon structure refinement, where my Rwork and Rfree are essentially stuck at 28 and 33, respectively. I have built the entire structure, including ligands, except for any solvent molecules. Here are the details for the data/structure: SG: P212121 Cell: 72 124 175 90 90 90 Res: 50-2.8 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.155 0.000 0.500 Distance to origin : 87.222 Height (origin=100) : 34.517 p_value(height) : 6.739e-04 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 6.739e-04. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Xtriage notes that the if the PTS is crystallographic, that C2221 is a possible SG (x+1/6, y, z+1/2). However, neither XDS or HKL picks orthorhombic C, and the indexing/integrating doesn't work if I force it. I should also not there is no twinning detected by either xtriage or twinning servers. I have done a number of things to try to resolve this: -rescaling in lower symmetry (P21 and P1) -rescaling in the PG P222 and letting the MR program decide the proper space group -shifting origin and re-refining -a number of different refinement protocols (TLS, optimized weights/adp, simulated annealing, several cycles of rigid body, etc.) I have used HKL2000 and XDS to index/integrate/scale the data, both yield the same results, with slightly different completeness and Rmerge values, but refining with either gives similar R factor values. Does any know of any other possible things I should try to refine this data? I am happy to provide additional information upon request. Thanks in advance for any help! Bret

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selectively remove bond length restraints on atoms
by Maxime Cuypers 15 Mar '12

15 Mar '12

hello, What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file: refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } } but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } } is it a good way to deal with the problem ? thanks in advance for your help. Maxime

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crystal packing pattern
by bsubedi＠btk.fi 15 Mar '12

15 Mar '12

Hi All, Could someone help me with a program/tool to see the pattern of protein packing in the crystal. I would like to make comparative study between regions of the protein in two different chains and if crystal packing has some effect on conformational alteration. Kind regards, World

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Reminder: BCA/CCP4 Summer School 2012
by Airlie McCoy 15 Mar '12

15 Mar '12

This is a reminder that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The course is suitable for PhD students in macromolecular crystallography who started in or before October 2011, and postdocs new to macromolecular crystallography. Please note that references from supervisors are also due by 1st May 2012, so don't leave your application until the last minute! For more information see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Pag…

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Transfer to new computer
by Colin Levy 15 Mar '12

15 Mar '12

Hi, Is it possible to transfer Phenix along with it's archive to a new computer? I have a fresh install of Phenix on the new machine and a copy of all the original files and folders from the old machine but cant figure how to point Phenix to the correct place. Thanks Colin

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March 15, 2012 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Mar '12

14 Mar '12

Dear Users, The deadline for May/June 2012 Collaborative Crystallography proposals will be *Mar 15, 2012. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ------------------------------------------------------------ ----------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2012 allocation period, proposals must be submitted by *March 15, 2012.* The deadline for CC proposals for the time period July/August 2012 will be May 15, 2012. Regards, Banumathi Sankaran

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