- phenixbb - phenix-online.org

Reproducibility of R-factors
by miket＠chem.ucla.edu 14 Sep '10

14 Sep '10

Hi All, I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong. Any insight/advice would be appreciated. Thanks, Mike Thompson -- Michael C. Thompson Graduate Student Yeates Lab Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Deposition of riding H
by Dr. Mark Mayer 14 Sep '10

14 Sep '10

Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better geometry (especially at low resolution). Phenix uses explicit riding H for refinement, and outputs these in the refined PDB. Refmac also uses riding H but does not output H coordinates. While depositing a series of structures refined at 1.4 - 2.75 A with Phenix got the following email from the RCSB, who asked I resupply coordinates without H for two of the structures. Since we can't see H even at 1.4 Å I don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why explicit H atoms used in refinement and geometry validation should be stripped from the file. FROM RCSB We encourage depositors not to use hydrogens in the final PDB file for the low resolution structures (> 1.5 A). Please provide an updated PDB file. We request you to use processed PDB file as a starting point for making any corrections to the coordinates and/or re-refinement. -- Mark

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Re: [phenixbb] Deposition of riding H
by Jeff Headd 14 Sep '10

14 Sep '10

Hi Mark, If hydrogens are used to arrive at a final refined model (whether riding or not) it is essential for the reproducibility of results that the H atom records be included in the deposited model. How B-factors are specified and some final atomic positions (such as rotatable methyl groups) are difficult or impossible to predict once removed, so without their deposition this information would be lost and any published statistics would not be reproducible as published. This point is illustrated in one of our recent papers: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 669-67. Further, there is no universal standard currently in use that specifies H bond-lengths (some use electron cloud distances, others neutron distances, some a mixture of both), meaning that without inclusion of H atom records (or at least a reference to which library was used) it is very difficult to know where the H atoms were placed. Thanks, Jeff On Tue, Sep 14, 2010 at 10:32 AM, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > Here's one for the community, which I'll post to both Phenix and CCP4 BBs. > > Where does the crystallographic community stand on deposition of coordinates > with riding hydrogens? > Explicit H are required for calculating all atom clash scores with > Molprobity, and their use frequently gives better geometry (especially at > low resolution). Phenix uses explicit riding H for refinement, and outputs > these in the refined PDB. Refmac also uses riding H but does not output H > coordinates. > > While depositing a series of structures refined at 1.4 - 2.75 A with Phenix > got the following email from the RCSB, who asked I resupply coordinates > without H for two of the structures. Since we can't see H even at 1.4 Å I > don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why > explicit H atoms used in refinement and geometry validation should be > stripped from the file. > > FROM RCSB > > We encourage depositors not to use hydrogens in the final PDB file for > the low resolution structures (> 1.5 A). Please provide an updated PDB > file. We request you to use processed PDB file as a starting point for > making any corrections to the coordinates and/or re-refinement. > -- > > Mark > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] autobuild : change reflection file mid-job?
by Thomas C. Terwilliger 14 Sep '10

14 Sep '10

Hi Bryan, Yes, I think to change the reflections file you will have to rerun the job as the reflections are read once in autobuild and propagated from there out. All the best, Tom T >> [it was inevitable..] >> >> if i swap the reflection file mid-job - THAT sounds like catastrophe : >> >> so does autobuild determine the format *only* from the .sca, .mtz affix? >> >> and it looks like reflections are read once at startup, and propagated >> from there out? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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autobuild : change reflection file mid-job?
by Lepore, Bryan 14 Sep '10

14 Sep '10

[it was inevitable..] if i swap the reflection file mid-job - THAT sounds like catastrophe : so does autobuild determine the format *only* from the .sca, .mtz affix? and it looks like reflections are read once at startup, and propagated from there out? -bryan

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Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 14 Sep '10

14 Sep '10

I will be out of the office starting 09/13/2010 and will not return until 09/15/2010. I have limited access to email and will respond to your message when I return.

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Re: [phenixbb] autobuild : change .seq mid-job?
by Thomas C. Terwilliger 13 Sep '10

13 Sep '10

Hi Bryan, I think that you can do this, though I have not tried it. You need to replace two files: 1. your original sequence file wherever it is "/wherever/.../myseq.dat 2 a file with the same name "myseq.dat" or whatever, in the directory AutoBuild_run_1_/TEMP0 I would expect all model-building after that to have the new sequence. (Note that runs that are already going as sub-processes will keep their sequences). Now if this is rebuild_in_place, this would not be a good idea. I am assuming it is rebuild_in_place=False, and so it should work... Let me know how it turns out, -Tom T >> i have a long autobuild job going. i'd like to change the .seq files as >> its going - if i keep residue 1 numbered, could this still be a >> catastrophe? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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autobuild : change .seq mid-job?
by Lepore, Bryan 13 Sep '10

13 Sep '10

i have a long autobuild job going. i'd like to change the .seq files as its going - if i keep residue 1 numbered, could this still be a catastrophe? -bryan

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debugger pdb
by Krista Joosten 10 Sep '10

10 Sep '10

Hi all, I'm working with Tom Burnley on the development of time_averaging.py. I would like to use the debugger pdb, but am not sure how to do this and whether it's possible. After some googling, I tried to hack into phenix.time_averaging adding -m pdb when the variable DEBUG==1, but I got the error message 'no module called pdb'. Bye Krista

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Beamtime at the ALS-BCSB beamlines
by Peter Zwart 10 Sep '10

10 Sep '10

Dear All, July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the 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. The main difference between local operation and remote operation, is the length of the network cable! This enhanced remote operation capability is coupled with 22hr 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. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service ( http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) or via twitter (@AlsRingStatus). Specific features are summarized below. Beamlines 5.0.1, 5.0.2, 5.0.3: -------------------------------------- Beamline 5.0.2 is equipped with a novel variable collimator allowing users to adjust the beamsize continuously and on the fly between 25 and 100 micron, both horizontally and vertically. With a collimator setting of 30x30 micron, typical exposures are around 1 to 2 second. The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Beamlines 8.2.1 and 8.2.2: ----------------------------------- 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 positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Data analyses in the BCSB is facilitated by software maintained by sbgrid ( http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional 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 contact BCSBBeamtime(a)lbl.govfor more information. 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 We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." 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 Research 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 SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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