August 2009 - phenixbb - phenix-online.org

Re: [phenixbb] phenix.refine special positions
by Ralf W. Grosse-Kunstleve 14 Aug '09

14 Aug '09

Hi Simon, To add to the previous answers, note that phenix.refine currently doesn't work well if you want to allow symmetry copies of your ligands to overlap. If you move to individual coordinate refinement you have to fix such ligands; i.e. it won't automatically repair bonds distorted by rigid-body refinement. Removing this limitation is on my to-do list. Ralf

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phenix.refine special positions
by Simon Kolstoe 14 Aug '09

14 Aug '09

Dear Pavel et al. Is there any way of defining a residue for rigid body refinement if a couple of the atoms are sitting on a symmetry axis? i.e. can I define the rigid body to be chain L but not the atoms that are giving the problems? I keep on getting the error: ================== Extract refinement strategy and selections ================= Some atoms selected for rigid body refinement are in special positions (listed below). Please remove these atoms from the rigid body selection and run refinement again. "ATOM 4 C4 A12 L 2 .*. C " Sorry: Atoms at special positions are within rigid groups. Thanks, Simon

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Shake
by esmael 13 Aug '09

13 Aug '09

Hi, Would be possible to only add "Shake" to the side-chain atoms during the refinement with Phenix? Thanks, Esmael

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phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
by Francis E Reyes 13 Aug '09

13 Aug '09

Hi all I ran xtriage on my dataset to 4.5.here's the relevant section pertaining to anomalous signal Analyses of anomalous differences Table of measurability as a function of resolution The measurability is defined as the fraction of Bijvoet related intensity differences for which |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 holds. The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data are processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. Note that this analyses relies on the correctness of the estimated standard deviations of the intensities. unused: - 90.6596 [ 0/1 ] bin 1: 90.6596 - 9.2614 [1371/1382] 0.0375 bin 2: 9.2614 - 7.3520 [1369/1376] 0.0033 bin 3: 7.3520 - 6.4230 [1380/1388] 0.0000 bin 4: 6.4230 - 5.8358 [1353/1359] 0.0016 bin 5: 5.8358 - 5.4176 [1367/1371] 0.0000 bin 6: 5.4176 - 5.0982 [1361/1369] 0.0000 bin 7: 5.0982 - 4.8429 [1378/1382] 0.0000 bin 8: 4.8429 - 4.6321 [1351/1359] 0.0000 bin 9: 4.6321 - 4.4538 [1383/1389] 0.0000 bin 10: 4.4538 - 4.3001 [1390/1393] 0.0000 unused: 4.3001 - [ 0/0 ] The full resolution range seems to contain a useful ammount of anomalous signal. Depending on your specific substructure, you could use all the data available for the location of the heavy atoms, or cut the resolution to speed up the search. If values larger than 0.05 are encouraging why is it telling me that the entire resolution contains a useful amount of anomalous signal? Did I process this incorrectly? 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

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General User Proposal Deadline for PX/SAXS at the ALS: August 15, 2009
by Peter Zwart 12 Aug '09

12 Aug '09

Dear All, August 15, 2009 is the deadline for the October - December 2009 Rapid Access Proposal cycle. (!!!!Please note that the ALS will be shut down in September, 2009.!!!!) Remote data collection is available on all beamlines at the Berkeley Center for Structural Biology (BCSB). The NX remote desktop technology provides the remote user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 24hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Beamlines 8.2.1 and 8.2.2: Both beamlines are now fully remote capable, which means that users are able control sample mounting, data collection and analysis from their home labs. This has dramatically increased the efficiency of data collection and significantly reduced the cost of protein crystallography experiments, since users no longer have to travel to the synchrotron. To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. As part of the beamline optics upgrades, a new toroidal focusing mirror was purchased and installed in beamline 8.2.1; new parabolic mirrors are currently being polished. When completed, the new optics will increase the brightness of beamline 8.2.1 by a factor of 4 to 5 and decrease the spot size to 30 microns, greatly facilitating structure solution on large macromolecular complexes. Beamlines 5.0.1, 5.0.2, 5.0.3: On Sector 5, improvements to the existing Berkeley Automounter sample handling system have dramatically improved both total capacity and reliability. Upgrades to the 5.0.1 and 5.0.3 monochromators have been completed. The operational energy of both beamlines has been increased, taking them above the Se K-edge and thus introducing a significant new Se SAD capability for experiments on Se derivatized proteins. The new monochromators also provide significantly better beam focus and performance under the increased power loads of ALS topoff operation. These improvements have been coupled with the introduction of enhanced positional feedback, diagnostic tools, and auto-alignment systems for the beamline components to improve the overall stability and quality of the beam delivered to users. Another mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology/Small Angle X-Ray Scattering (SAXS)." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for January-February 2010 beamtime at the Advanced Light Source, please submit a General User proposal by November 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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xtriage
by Francis E Reyes 12 Aug '09

12 Aug '09

Hi all I love the fact that xtriage can measure anomalous signal, but can it also do a quick check for isomorphous differences (with and without anomalous signal) similar to scalepack? Is there a phenix utility that can do this? 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

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duplicated label
by Jianghai Zhu 12 Aug '09

12 Aug '09

Hi, I am using phenix.refine-125 to do a MLHL refinement. I got an error at the end of the refinement while it was trying to exporting results. "Sorry: Duplicate mtz_label_amplitudes:FOFCWT". The output map_coeffs.mtz file is corrupted and the next def file is blank. The refined pdb file seems to be fine. Anyone knows how to fix this problem? Thanks. -- Jianghai

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where are the optimized wxc_scale and wxu_scale when optimize_wxc_scale and optimize_wxu_scale = True?
by Francis E Reyes 07 Aug '09

07 Aug '09

Hi all I went through the time to optimize_wxc and optimize_wxu to help pull out some density for ligands (i.e. all sequence assigned residues are built). However, it would be nice if the resulting .def was updated with the optimized wxc and wxu. Where are those values? I didn't think for wxc it was scale=XX in the following lines.. r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles= 0.70 scale= 7.00 r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles= 0.96 scale= 8.00 ... etc Refining with the scale= value that phenix ultimately chose didn't work form me (resulted in awful geometry and high r/rfree). 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

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Re: [phenixbb] Let's talk about maps...
by Dr. Mark Mayer 07 Aug '09

07 Aug '09

Hi Pavel, It would be really nice if the Electron density maps section in the online docs for phenix.refine http://www.phenix-online.org/documentation/refinement.htm#anch70 was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb. Mark --

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Re: [phenixbb] Autobuild error (FIXED)
by youssef ben ammar 07 Aug '09

07 Aug '09

Thanks for all replies, Autobuild error linked to the long path was solved based on the suggestion of Ben Eisenbraun (thanks Ben). I reinstalled tcsh, but only that did not solve the problem. So, I deleted csh from the path and kept only the newly installed tcsh after that everything is running perfectly. Youssef

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