- phenixbb - phenix-online.org

Beam Time at BCSB beamlines in Berkeley
by Peter Zwart 13 Mar '08

13 Mar '08

============================================================= Synchrotron Beam Time available for Macromolecular Crystallography at Berkeley Center for Structural Biology Beamlines (5.0.1, 5.0.2, 5.0.3, 8.2.1 and 8.2.2). The ALS is now accepting General User applications for May/June ============================================================= The Berkeley Center for Structural Biology (BCSB) operates five beamlines at the Advanced Light Source in Berkeley. Beamlines 5.0.1, 5.0.2 and 5.0.3 are equipped with the Berkeley Automounter system. Beamline 8.2.2. has a Rigaku Actor sample mounter capable of handling Rigaku, unipucks and ALS style pucks. Beamlines 5.0.2, 5.0.3, 8.2.1 and 8.2.2 have large 3x3 Q315 or Q315r CCD detectors. Beamlines 5.0.2, 8.2.1 and 8.2.2. are MAD stations, whereas 5.0.3 and 5.0.1 are fixed energy beamlines at the Se high energy remote, suitable for Se-SAD experiments. The beamlines generate between 1.5x10^11 and 8x10^11 photons per second of flux into a 100 micron collimator at 1.5 mrad divergence. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for beamtime at these, or any other ALS macromolecular crystallography beamlines, please submit a General User proposal by March 15, 2008 in order to be considered for the May-June schedules. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize You can also request access to any open beam time on the five BCSB beamlines by e-mailing our scheduler at SLOrtega(a)lbl.gov. Any industrial or academic group interested in becoming part of the Participating Research Team for beamlines 5.0.1 and 5.0.2 should contact the Head of the BCSB (Paul Adams: PDAdams(a)lbl.gov, 510-486-4225). (Please note that executed user agreements and proprietary fees, if applicable, must be received at least five working days prior to scheduled beam time.) -- Peter Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron road, Berkeley, CA-94720 Cell: +1 510 289 9246 Fax: +1 510 486 5664

1 0

Collaborative Crystallography
by Banumathi Sankaran 12 Mar '08

12 Mar '08

The Berkeley Center for Structural Biology (BCSB) is pleased to announce a new Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists are able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program provides a number of benefits to researchers: * Obtain high quality data and analysis through collaboration with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. CC proposals go through the regular ALS General User proposal review process. They are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the projects to fit into the available resources. Please note that only non-proprietary projects are currently being accepted. In keeping with similar programs the BCSB staff researchers who participate in data collection and/or analysis should be appropriately acknowledged as authors on publications and/or 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 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 Mai/June, 2008, proposals must be submitted by March 15, 2007. Questions: For comments or questions, feel free to contact Banumathi Sankaran (BSankaran(a)lbl.gov) or Gari Kloss (MKloss(a)lbl.gov)

1 0

refine error when optimize_wxc w/o optimize_wxu turned on
by shi jiahai 11 Mar '08

11 Mar '08

Hi, Dear all, I was using phenix.refine to refine the structure. Once I turned on optimize_wxc w/o optimize_wxu, the job failed with the following message. ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/Application/phenix/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc The phenix I used is the latest version, 1.3b rc6. The platform is intel-linux-2.6 redhat-e4. Python is 2.4.2 Could anyone please tell me what the problem is? Thank you very much! -- Best Regards, Shi Jiahai

2 2

autobuild errro message
by Christine Gee 05 Mar '08

05 Mar '08

Hi I was using phenix.autoMR and when it tried to go on to autobuild the job ended with the following error message AutoBuild Input failed can only concatenate list (not "str") to list There are two molecules in the asymmetric unit. I tried running phenix.autobuild with the output pdb from molecular replacement and got the same message. The file looks OK to me though. Can you tell me what the problem is? Regards Christine

2 1

problem compiling phenix 1.3 beta rc3
by Melody Lin 05 Mar '08

05 Mar '08

Dear all, I have a problem compiling phenix-1.3beta-rc3 on my Mac OSX tiger ppc. I downloaded the tar file under the sbgrid directory and issued command "sudo ./install" to compile it after unzipping. Everything went OK until the last step when the installer is trying to compile phenix components, ands says it will take an hour, but in 2 minutes it reports failure for the compilation. Could anyone suggest what problem this is? Did I download the wrong tar file? Your input is greatly appreciated! Best, Yan

5 6

Question about occupancy refinement of riding hydrogens
by Schubert, Carsten [PRDUS] 04 Mar '08

04 Mar '08

I just noticed that occupancies of riding hydrogens are being refined by default, in fact I am unable to turn this feature off (CCI-APPs from Jan-8). I was just (very naively) wondering what is the rationale behind this? The B-factor refinement for riding hydrogens is already enabled and should take care of this or not? It looks a bit odd to have hydrogens with occupancy 0.9 sitting on a carbon with occupancy 1.0 at 2.0 A resolution. Cheers Carsten

2 1

Enhancement request for map formats
by Schubert, Carsten [PRDUS] 04 Mar '08

04 Mar '08

Hi, I was wondering if it would be possible to have the choice of generating ccp4 maps in phenix.refine. This type seems to be best compromise so far between compatibility and size. The xplor type ascii maps are 10x the size and do not offer any advantage in a homogeneous OS environment. Converting the maps after the fact is one more step I am trying to eliminate. Cheers Carsten

2 4

Possible to rebuild only certain residues in a molecule?
by Francis E Reyes 04 Mar '08

04 Mar '08

All Can the rebuild process be directed to rebuilding specific residues in the molecule? Can this be extended to build multiple models of a given set of residues? Thanks FR --------------------------------------------- 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

2 1

problem with a twinned data set
by Pascal EGEA 02 Mar '08

02 Mar '08

Hi All This a question of general Crystallography and use of Phenix to deal with twinned data. I am having difficulties with a data set. We have data (2.6 ang resolution) that can be scaled and reduced in P222 with a Rmerge of 7%, the systematic absences show a screw axis ( it is P22(1)2). However MR in Phaser failed in this orthorhombic settings when searching for 2 molecules of the complex in the AU. If we reduce and scale the data in P2(1) and look at the diffraction pattern in HKLVIEW there is a /mmm symmetry. In the monoclinic P2(1) setting we can find 4 molecules of the complex (by MR in Phaser) and can refine it with Phenix to a Rfac/Rfree of 28%/34%. 2 molecules have good electron density whereas the two other ones have one of their domain very poorly defined in density. This is looking very suspicious to me and I am wondering if this refined structure is partially wrong? Meanwhile I used phenix.triage on the data processed in P222 and I am confused with the output. ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 3.36 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------ ------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------ ------- | PM | 4-fold | 2.851 | 0.000 | 0.013 | - l,k,h | ------------------------------------------------------------------------ ------- M: Merohedral twin law PM: Pseudomerohedral twin law 0 merohedral twin operators found 1 pseudo-merohedral twin operators found In total, 1 twin operator were found --------------------------------------------- Analysing possible twin law : -l,k,h --------------------------------------------- Results of the H-test on acentric data: (Only 50.0% of the strongest twin pairs were used) mean |H| : 0.368 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.194 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.132 Estimation of twin fraction via cum. dist. of H: 0.115 Britton analyses Extrapolation performed on 0.14 < alpha < 0.495 Estimated twin fraction: 0.127 Correlation: 0.9955 By comparison if I run the detect_twin routine of CNS it tells me that they are no merohedral twin laws for the point group 222 (using the statistical method of Yeates) ? This is confusing me quite a bit. Assuming that the twinning law suggested by Phenix is correct how should I proceed? I have noticed the section concerning refinement using twinned data in Phenix phenix.refine data.hkl model.pdb twin_law="-k,-h,-l" detwin.map_types.aniso_correct=true but It seems I only have a MR solution in P2(1) but not in P222(1) so how can I refine in P222(1) I will greatly appreciate your input, many thanks. Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

4 4

ligand refinement - elbow
by Christine Gee 01 Mar '08

01 Mar '08

Hi Its taken me a while to get around to it, but I just ran elbow to create a cif file etc for my inhibitor, but the bond lengths are quite different from what I got from the PRODRUG server, and it seems that the pdb file I got out of elbow has a few problems (COOT doesn't join up the aromatic ring for example because the carbons are now too far away on one part of the ring). I was wondering how the bond lengths are selected? It seems it is giving the aromatic carbons a bond length of 1.5, when my previous file (and phenylalanine for example have 1.3). Also, I still am not 100% sure how to add the CONNECT information to make the ligand able to covalently bind to the protein. Regards Christine

3 2