- phenixbb - phenix-online.org

hydrogens in low resolution structure refinement
by Stefanie Krieg 16 Nov '07

16 Nov '07

Dear all! I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be? Thanks in advance! Stefanie

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Re: [phenixbb] use of wavelength_list=
by Tom Terwilliger 12 Nov '07

12 Nov '07

Hi Bryan, phenix.autosol uses the values in wavelength_list to guess scattering factors if you do not supply values for scattering factors. All the best, -Tom T At 03:21 PM 11/10/2007, you wrote: >does phenix use the 'wavelength_list=' command line flag in calculations? >or is it used for no more than data set labeling e.g. derivatives, as >solve works? > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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use of wavelength_list=
by Bryan W. Lepore 10 Nov '07

10 Nov '07

does phenix use the 'wavelength_list=' command line flag in calculations? or is it used for no more than data set labeling e.g. derivatives, as solve works? -bryan

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Collaborative Crystallography Program - Advanced Light Source
by Paul Adams 09 Nov '07

09 Nov '07

The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects 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 submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/ Initialize. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February, 2008, proposals must be submitted by November 15, 2007. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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Re: [phenixbb] phenix.autobuild opinion on sequence file
by Tom Terwilliger 08 Nov '07

08 Nov '07

Hi Bryan, I haven't tried your approach, but my guess would be that the correct sequence file will be the better way to go... The side chains are fitted after building main-chain so the sequence is not going to affect the main-chain build in any direct way (though the sequence will help the wizard in identifying and correcting places where loops are built with the wrong number of residues). -Tom T At 01:32 PM 11/8/2007, you wrote: >i was thinking about giving phenix.autobuild a poly-Ser/Gly,Ala-intact (or >other incomplete variant) _sequence_file_, so it doesn't inter alia put >arginine into strands... though the solvent content will be imprecise.. > >has anyone noticed if such a trick was more/less favorable to the (proper) >complete sequence approach? any pertinent detail or criticisms >appreciated. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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phenix.autobuild opinion on sequence file
by Bryan W. Lepore 08 Nov '07

08 Nov '07

i was thinking about giving phenix.autobuild a poly-Ser/Gly,Ala-intact (or other incomplete variant) _sequence_file_, so it doesn't inter alia put arginine into strands... though the solvent content will be imprecise.. has anyone noticed if such a trick was more/less favorable to the (proper) complete sequence approach? any pertinent detail or criticisms appreciated. -bryan

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problem finding large no of sites in high symmetry
by Banumathi Sankaran 08 Nov '07

08 Nov '07

Hi, I am working with a data set collected in P23 space group. I am expecting 23 Se sites. Hyss gives me warning:run time error for finding large no of site. I did not interupt the run. I waited for 1hr and still it could not find sites. Shelx gave me out of 100 solutions only one had good CC and found 15 sites. IS there a way that this problem can be solved in hyss ? Thanks Banu

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Re: [phenixbb] Advice about phasing procedure and phase extension in AutoSol-AutoBuild
by Tom Terwilliger 08 Nov '07

08 Nov '07

Hi Carsten, >1. can I input known HA-positions into the AutoSol wizard to help >Hyss find other positions? Does Hyss actually eliminate bogus sites? >Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a >B-factor of one, but does not toss them. How does Hyss handle this situation? As far as I know, you cannot seed hyss with sites. If you have SAD data, try the autosol wizard which uses Phaser. Phaser has a good LLG map algorithm for finding addtional sites. >2. What is the best way to handle phase extension in the Wizards, >how would one go about this? I would like to fine-tune the >resolution steps myself as not to jump to far out to higher resolution. The wizards use the defaults for phase extension in resolve. If you want to fine-tune the resolution steps you can say, resolve_command_list=" 's_step 0.05 ' " Note the 2 sets of quotation marks.... This will use steps of 0.05 A for phase extension (type phenix.autobuild --help resolve_command_list for documentation of this command) >3. What quality indicators should I look at? A couple of FOMs in the >resolve runs were in the region of 0.7, but the maps were not >interpretable and resolve failed to build anything. Anything else I >should look at? Best is the R-factor at the end of density modification. If it's around 0.30 you are doing well. 0.4 is bad, 0.25 is great. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Advice about phasing procedure and phase extension in AutoSol-AutoBuild
by Schubert, Carsten [PRDUS] 08 Nov '07

08 Nov '07

Hi, I am trying to bootstrap my way into a couple of weak derivatives using a combination of Solve and the AutoSol and AutoBuild wizards. I have probably one or two fairly weak diffracting derivatives (~3A) with low FOMs (~0.3) from Solve, the native extend to ~2.A. I have a couple of questions about how to best proceed with the phasing procedure using either the wizards or a Solve/Resolve combination. 1. can I input known HA-positions into the AutoSol wizard to help Hyss find other positions? Does Hyss actually eliminate bogus sites? Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a B-factor of one, but does not toss them. How does Hyss handle this situation? 2. What is the best way to handle phase extension in the Wizards, how would one go about this? I would like to fine-tune the resolution steps myself as not to jump to far out to higher resolution. 3. What quality indicators should I look at? A couple of FOMs in the resolve runs were in the region of 0.7, but the maps were not interpretable and resolve failed to build anything. Anything else I should look at? Thanks Carsten

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Re: [phenixbb] autobuild 'hires_file'->now FreeR flags, merging, ...
by Tom Terwilliger 07 Nov '07

07 Nov '07

Hi Bryan, >On Tue, 6 Nov 2007, Thomas C. Terwilliger wrote: > > The problem is in that version of phenix. I'm sorry about that! Can you > >that solved it, thanks. Oh good. > >> [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag > >> 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases > >> will be extended to a high resolution limit as found in w1.sca? (vide > >> infra) > > > > Yes, that is correct. > >ok, then i have to ask - is phenix merging each reflection? i.e, i >wouldn't want to do this w/ a derivative and hi-res native, right? Yes, it is merging in each reflection, if I understand the question. Yes, you might do it with phases from a native+derivative and a hi-res native. (We're only talking about doing this in autobuild, after you have "experimental" phases from something.) -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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