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Re: [phenixbb] General user proposal deadline May 15, 2010
by Peter Zwart 12 May '10

12 May '10

Dear All, Just a reminder that May 15, 2010 is the deadline for the July-August 2010 Rapid Access Proposal cycle for PX beamtime at the ALS. The BCSB beamlines (5.0.1,5.0.2, 5.0.3, 8.2.1 & 8.2.2) can all be operated remotely and are all equipped with ADSC Q315(R) detectors. Beamlines 8.2.2, 8.2.1 and 5.0.2 are tuneable stations whereas 5.0.1 and 5.0.3 are fixed-wavelength beamlines. Control software for the beamlines features an interface allowing ultra high-throughput screening, automated annotation of diffraction quality and on the fly indexing and collection strategy feedback. The automounters in use on sector 5 support the unipuck and the ALS puck (both commercially available at http://www.crystalpositioningsystems.com). Beamlines 8.2.1 and 8.2.2. support in addition to the uni- and ALS puck the Rigaku system (http://www.rigaku.com/) To submit a proposal, please go to the ALS website link listed below: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize Thank you, Stacey Ortega 510-495-2450

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suggested change to OS X GUI ?
by Mark Saper 12 May '10

12 May '10

Dear Nate, Not a major problem, but would you consider changing the keyboard shortcut for "View all settings..." from command-A to option-command-A? I keep typing command-A to select all which is the usual binding for this key. Thanks, Mark

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May 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 10 May '10

10 May '10

Dear Users, The deadline for May/June 2010 Collaborative Crystallography proposals will be *May 15, 2010. * ------------------------------------------------------------------------ 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 July/August 2010 allocation period, proposals must be submitted by *May 15, 2010.* The deadline for CC proposals for the time period Sep/October 2010 will be July 15, 2010. Regards, Banumathi Sankaran

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mac os x installation binary files
by xaravich ivan 07 May '10

07 May '10

Hi Phenix users, I am trying to install phenix in my Mac OS X and after getting the .tar file and running install i get this message (screen shot attached) Could anyone help the newbie? Thanks, Ivan

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Rigid body refinement question
by Simon Kolstoe 06 May '10

06 May '10

Dear phenixbb, What do I need to change in my .def file if I want to refine chain A-E of a structure as per the defaults but specify a single chain (in my case chain L) for just rigid refinement in all cycles? I had a look at the manual page (http://www.phenix-online.org/documentation/refinement.htm ) but didn't find it too clear. Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek --------------------------------------------------------------

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weight non-bonded contacts during rigid body refinement
by Kenneth Verstraete 06 May '10

06 May '10

Dear all, I wonder how I can set the weight for non-bonded contacts to zero to prevent clashes during rigid body refinement. Thank you for your comments. Kenneth Verstraete

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phenix-dev-386 Sorry: Sorry, unknown file or keyword: refinement_eff_file=refinement.eff for AutoBuild
by Francis E Reyes 06 May '10

06 May '10

Was this keyword removed/renamed for the command line version of AutoBuild? http://www.phenix-online.org/documentation/autobuild.htm says I should be able to specify refine_eff_file. Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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sugar behaving sourly
by Patrick Loll 05 May '10

05 May '10

Hi, I'm refining a structure with an unusual monosaccharide. I generated a library for this sugar from PRODRG, and it looks OK, at least to my eye. Certainly the obvious parameters like bond angle restraints seem normal. However, when I refine with phenix, the sugar's C6 methyl group gets pushed out of density and assumes a very unnatural angle. Now, it turns out that there are two copies of this molecule in the AU, and the other copy looks fine after refinement. Moreover, I can load my library into Coot, and when I use it to refine the sugar's position or regularize its geometry, it works just fine; and when I run phenix.pdbtools --geometry_regularization and supply my library, the resulting structure has nice geometry. These three observations lead me to believe that there's nothing inherently wrong with my library. There are no steric clashes that would tend to push this methyl group out of whack (but just to be sure, I removed all nearby atoms and repeated the refinement, with the same result). I should mention that this refinement is at ca. 1.8 Å, and the density for the sugar looks quite nice. Any suggestions? Cheers, Pat Loll --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Input NCS operators for AutoBuild
by Mark A Saper 05 May '10

05 May '10

This questions may be best answered by Tom. Does anyone know how to generate a custom NCS definition file that AutoBuild will read from the refinement format? The parameter is input_ncs_file = I used phenix.simple_ncs_from_pdb to generate 3 ncs format files. But I could not figure out how to make the program use my definitions. In any case simple_ncs_from_pdb outputs 3 formats in ./phenix/tmp: simple_ncs_from_pdb.ncs simple_ncs_from_pdb.ncs_spec simple_ncs_from_pdb.resolve I tried the last one, but it has no residue or chain specification. Should I use the .ncs_spec? The first one is for phenix.refine. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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Re: [phenixbb] NCS problems using phenix GUI on a Mac
by Mark A Saper 05 May '10

05 May '10

John, I am having the exact same problem. I need the NCS parameters in a format suitable for AutoBuild which I think is different than phenix.refine. Are you trying to use phenix.simple_ncs_from_pdb routine in GUI? Let me know if you have made any progress. Thanks, Mark > Hello, > > I am having difficulties defining NCS parameters using the GUI > interface (Mac 10.4.11; phenix 1.6-289). > > Phenix will automatically select NCS restraint groups and use them > during refinement. But if I edit the automated selections to my > liking then click on Update and Save, the refinement runs with the > original parameters unedited. I have tried reading in a ncs.param > file, but it does not get read during the refinement run. Also, an > intermittent problem with this GUI is that I am not allowed to "Add" > a new restraint group. When I click this button, it just clears out > the selections on the last group, and does not add a new group. Any > ideas? > > Thanks. > > Best, > John > > -- > John Pascal, PhD ph 215.503.4596 > Assistant Professor fx 215.923.2117 > Thomas Jefferson University > Biochemistry & Molecular Biology > 233 South 10th Street, BLSB 804 > Philadelphia, Pennsylvania 19107 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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