September 2010 - phenixbb - phenix-online.org

nqh-flip option
by Christian Roth 16 Sep '10

16 Sep '10

Dear all, I put manually in the parameterfile from the gui the option nqh_flips=True. After the run starts, a popup comes up claiming about an invalid unsupported option and the refinement stops without producing any file, even not a log-file. Does the nqh option not longer exists or what happend here? I use at the moment phenix 1.6-289. Thanks for your help. Christian

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Re: [phenixbb] autobuild : MSE's keep coming back
by Thomas C. Terwilliger 16 Sep '10

16 Sep '10

Hi Bryan, Hmmm...I can't seem to make it happen with my standard inputs. Can you possibly send me directly (terwilliger(a)lanl.gov) your AutoBuild_run_1_/autobuild.eff file or better yet that plus your input files and I'll try that out here? Thanks a lot, All the best, Tom T >>> are you using a recent version? >> >> v1.6.4 release tag 486 >> >>> is this rebuild_in_place or not? >> >> well, i did not specify rebuild_in_place, however, i poked around and can >> see that autobuild has switched on rebuild_in_place so i call that a >> "yes". >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] autobuild : MSE's keep coming back
by Lepore, Bryan 15 Sep '10

15 Sep '10

> are you using a recent version? v1.6.4 release tag 486 > is this rebuild_in_place or not? well, i did not specify rebuild_in_place, however, i poked around and can see that autobuild has switched on rebuild_in_place so i call that a "yes". -bryan

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Re: [phenixbb] [ccp4bb] Deposition of riding H
by Dr. Mark Mayer 15 Sep '10

15 Sep '10

>However this thread appears to have reached the point where not much new >ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the experts weigh in on this. I've learned a lot, and clearly there is no consensus. As one of the vast majority of crystallographers dependent on all the hard work that program developers undertake to support structural biology, I'm happy to follow advice given by the developers of the various programs I use, and for Phenix the current advice is to deposit with riding H. -- Mark

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Re: [phenixbb] [ccp4bb] Deposition of riding H
by Felix Frolow 15 Sep '10

15 Sep '10

Pavel, Shelxl is working in correct coordinates - fractional... Many things are easier in fractional coordinates. Are you sure that Phenix does not go orthogonal -> fractional -> orthogonal in internal calculations? When fixing of parameter is made in fractional coordinates it does not produce confusion. Shelxl also make fractional -> orthogonal (AKA PDB) which is also correct. Constrain is not transferred there. BTW Shelxl knows symmetry very well and will constrain atoms that occupying symmetry elements. Shortly Shelxl knows crystallography best. When you will see number of lines in Shelxl Fortran code ( do not kill Fortran to early) you will be surprised. There are not so many of them. No graphical user interface yet, but COOT is of great help. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 15, 2010, at 19:11 , Pavel Afonine wrote: > Hi Tim, > >> The pdbe.org, for example allows to upload auxiliary files and in my opinion the >> uploading of the final .ins-file (not the .res-file!) should be made mandatory >> in the case of shelxl refinement. >> >> Since coot has now become utterly convenient even for shelxl refinement, there >> is no reason one should not deposit the .ins-file ([flame] and the PDB-file >> probably for legacy reasons [/flame]). > > I was always wondering but never had a good occasion to ask (my Shelxl knowledge is limited and may be outdated so I apology in advance if my questions are too dummy; also I realize that I'm asking a non-CCP4 question on CCP4bb for which I apology again): > > - how .ins file encodes the information about NCS groups used in refinement (atom selection for NCS groups, restraint weights for different groups, etc? > > - how .ins file encodes the information about TLS (again, atom selections for TLS groups, TLS matrices, etc)? Related, does it have a concept of having TLS and other components to the total atomic displacement parameter (ADP)? > > - If I recall it correctly, to fix (=not refine) a certain parameter (say occupancy or B-factor) in Shelxl you need to add a number 10 to it. Is it true? IMHO, this might lead to confusion if such a file gets deposited to PDB. > > All the best! > Pavel.

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How does phenix.fmodel treat isotropic and anisotropic B?
by zhangh1＠umbc.edu 15 Sep '10

15 Sep '10

Hi, I am doing a phenix.fmodel calculation for a PDB structure containing anisotroipc B. If I understand it correctly, the B factor is composed of both the isotropic B for ATOM line (Biso) and the anisotropic B from ANISOU line (Uani): Fc=sigma ( fi * exp (-Biso*s*s) * exp (-st*Uani*s) * exp (i*r*s) ) Please correct me if the above equation is wrong. I also noticed that in PDB, the Uani (after scaling by 10^-4) is generally much smaller than Biso. So I assume that Biso has a much bigger contribution than Uani, the latter only implying the vibrational anisotropicity. However, I did a test calculation by setting all Bio to 0 whereas keeping Uani unchanged. Due to the above assumption, I expected the results should be very different from the native structure; however, coot told me they were just so close... Maybe I am wrong somewhere... Best Regards, Hailiang

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Sep 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Sep '10

14 Sep '10

Dear Users, The deadline for Nov/Dec 2010 Collaborative Crystallography proposals will be *Sep 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 Nov/Dec 2010 allocation period, proposals must be submitted by *Sep 15, 2010.* The deadline for CC proposals for the time period Jan/Feb 2010 will be Nov 15, 2010. Regards, Banumathi Sankaran

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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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