- phenixbb - phenix-online.org

cut-out mtz edition
by Dialing Pretty 26 Apr '12

26 Apr '12

Dear All, I just cut out a fragment of chain and the corresponding electron density from the whole molecule. Will you please give me some suggestion on how to edit the attached file so that those electron density not from the protein fragment can be erased? Or do you have other methods to produce high quality figure which just shows the fragment chain and the fragment eletron density? Cheers, Dialing

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Geometry Restraints - UPDATE
by Mario Sanches 25 Apr '12

25 Apr '12

Last week I asked a question about geometry restraints at low resolution. I would like to thank you all that took the time to answer, specially Pavel for looking at the data. First, here is the original question: __________________________________________ I am refining a low resolution structure (2.9A) using phenix.refine. As I continue the refinement Rwork/Rfree are dropping but my geometry statistics in general are very bad. My clashscore is getting worst and the RMS(angle) is really high. I have tried to play with the "wxc_scale" parameter and also ran phenix selecting the "Optimize X-ray/ADP weight" option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of ~190. Is there a known procedure to deal with this? I feel that my geometry weighing term is too loose but I don't know exactly how to tighten it other than decreasing the wxc_scale parameter. I have gone and manually corrected bad positions before but given the low resolution nature of the structure the clashes tend to be reestablished during refinement. Thank you in advance for your help, __________________________________________ It turns out that the reason to my nightmares was a highly anisotropic dataset. When I tried to fix geometry related problems in coot, phenix.refine was twisting the geometry back again, probably because it was trying to fit a lot of noise due to the anisotropy. Everything was getting worst, geometry, clashscore, and Ramachandran. Pavel finally corrected it by using this server: http://services.mbi.ucla.edu/anisoscale/ I should have been more diligent regarding that, since I could clearly see that my data was anisotropic from the diffraction images. I just didn't know how important this parameter could be. Anyways, phenix.xtriage will tell you if your data is anisotropic. The lesson is to pay attention to it. In my case, the quality of the electron density improved considerably, the geometry improved massively (manual intervention in coot was absolutely necessary, but now it stays correct after I manually fix the problems), clashscore lowered, etc. As a side note, it worked better without hydrogens in my case than with. It is certainly a parameter to try if you are having problems. Thank you all again for the tips. Mario Sanches -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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labelit.index with compatibility file
by "Weiergräber, Oliver H." 24 Apr '12

24 Apr '12

Hello, I have used labelit.check_pdb_symmetry to evaluate a P1 dataset and model for possible higher symmetry. C2 turned out to be a candidate solution. When I used the new asymmetric unit content file (xyz_coset0.pdb) to force indexing in the new SG: labelit.index /path/to/my/images/template_####.img 1 90 compatibility_file=xyz_coset0.pdb, the program crashes with AttributeError: 'NoneType' object has no attribute 'mosaicity_spot_coverage' This happens with the version included in phenix-1.7.3 as well as with the latest standalone labelit package. Any ideas what might be causing this? Maybe the new cell fails to refine? It is absolutely possible that forcing the higher symmetry SG leads to significant positional rmsd - I actually believe that P1 is correct, but it's definitly not far from C2. Best regards ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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twinning question
by Patrick Loll 20 Apr '12

20 Apr '12

Dumb question here: When one runs the various twinning tests (e.g. phenix.xtriage), is one meant to use data processed in the higher symmetry SG, or the lower symmetry SG? A concrete example: I can process a data set in a 622 point group w/ reasonable merging statistics, but an abnormally low solvent content raises my suspicions. So do I process as P6, and submit these data to the twinning test? Or do I submit the data processed as P622? Pat --------------------------------------------------------------------------------------- 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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Geometry Restraints
by Mario Sanches 19 Apr '12

19 Apr '12

I am refining a low resolution structure (2.9A) using phenix.refine. As I continue the refinement Rwork/Rfree are dropping but my geometry statistics in general are very bad. My clashscore is getting worst and the RMS(angle) is really high. I have tried to play with the "wxc_scale" parameter and also ran phenix selecting the "Optimize X-ray/ADP weight" option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of ~190. Is there a known procedure to deal with this? I feel that my geometry weighing term is too loose but I don't know exactly how to tighten it other than decreasing the wxc_scale parameter. I have gone and manually corrected bad positions before but given the low resolution nature of the structure the clashes tend to be reestablished during refinement. Thank you in advance for your help, -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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inverting a set of phase angles
by Mooers, Blaine H.M. (HSC) 19 Apr '12

19 Apr '12

Does phenix have a reflection file utility for correctly inverting a set of phase angles? Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Letter address: Shipping address: P.O. Box 26901, BRC 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73190 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu<mailto:[email protected]> webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…

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torsion NCS and SA
by dirk.reinert＠boehringer-ingelheim.com 19 Apr '12

19 Apr '12

Dear all, Is it safe to use torsion NCS (refinement.ncs.type="torsion") and torsion SA (refinement.main.simulated_annealing_torsion= "true") as a default? Thanks for advice, Dirk --- Dr. Dirk Reinert Boehringer Ingelheim Pharma GmbH & Co. KG Dept. Lead Identific. and Optim. Sup. Ge Tel.: +49 (7351) 54-97892 Fax: +49 (7351) 83-97892 mailto:[email protected] Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein; Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender), Ursula Fuggis-Hahn, Ralf Gorniak, Michael Klein, Dr. Martin Wanning; Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein; Registergericht Mainz: HR B 23260 Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited.

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Can the Update Waters routine ignore specified waters?
by John Pascal 19 Apr '12

19 Apr '12

Hello All, While using Update Waters in the phenix GUI, several waters that have been defined around a metal binding site are removed. I am happy with the placement of these waters - can I specify somewhere that Update Waters should leave them alone? and that their positions, etc. are still refined during the run? Thanks. Best Regards, John -- *John M. Pascal, PhD* Assistant Professor Department of Molecular Biology & Biochemistry Kimmel Cancer Center Thomas Jefferson University 233 South 10th Street, BLSB Room 804 Philadelphia, PA 19107 Email: John.Pascal(a)KimmelCancerCenter.org <mailto:[email protected]> Phone: (215) 503-4596 Fax: (215) 923-2117

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(no subject)
by Tom Burnley 18 Apr '12

18 Apr '12

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Re: [phenixbb] Bulk Solvent
by Nathaniel Echols 17 Apr '12

17 Apr '12

Garib's response below, since the server wouldn't let him post. ---------- Forwarded message ---------- From: Garib N Murshudov <garib(a)MRC-LMB.CAM.AC.UK> To: "Steiner, Roberto" <roberto.steiner(a)kcl.ac.uk> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> Date: Tue, 17 Apr 2012 18:11:24 +0100 Subject: Re: [phenixbb] Bulk Solvent Dear all I cannot say much without data. Only thing I can say that there were some problems in some of the versions in 5.5, and there are some improvements in recent versions. 5.7 series may perform better. Before claiming that improvement is due to particular feature I would do a little bit more analysis. regards Garib On 17 Apr 2012, at 18:03, Steiner, Roberto wrote: difference density on the backbone can also arise (more often) due to suboptimal ADP refinement/restraints..or a bug in a particular build.. best wishes roberto PS I cc-ed this email to Garib in case he's got some info specific for 5.5.0102 On 17 Apr 2012, at 17:22, Timothy Springer wrote: As I said, I cant say that, it is a guess based on two facts. 1) Looking at the output of refinement steps, and seeing that the largest decrease in R during refinement comes in the bulk solvent correction step. 2) It is also based on the common occurrence in the Refmac but not Phenix maps of negative difference density on backbone. This is a symptom of errors in bulk solvent correction. Tim On Apr 17, 2012, at 12:06 PM, Steiner, Roberto wrote: Hi Tim, How can you say the difference is really down to bulk solvent correction? there's several other parameters that affect differences in R factors.... Just curious R On 17 Apr 2012, at 16:27, Timothy Springer wrote: no, it just takes me two years to write up sometimes--- So this is a historical question. But there is a ref in that powerpoint to following ref. If this was implemented in Phenix and not Refmac 2 years ago, I should cite it. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):850-5. Epub 2005 Jun 24. A robust bulk-solvent correction and anisotropic scaling procedure. Afonine PV, Grosse-Kunstleve RW, Adams PD. Source Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA. pafonine(a)lbl.gov Tim On Apr 17, 2012, at 11:18 AM, Jeff Headd wrote: Hi Tim, If you are using Phenix 1.5.2, that would not have had the new bulk-solvent model that Pavel is talking about. Are you using that old of a version for your tests? Jeff On Tue, Apr 17, 2012 at 8:07 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > > Hi Tim, > > this is because recently (a few weeks ago) we introduced a novel bulk-solvent model and a new overall anisotropic scaling procedure. > > Some detailed overview is here: > > http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf > > This is going to be published soon. > > Pavel > > > On 4/17/12 7:59 AM, Timothy Springer wrote: > > In one of the structures I have refined, I found phenix 1.5_2 gave 1 to 1.5% lower Rfree and Rwork than REFMAC 5.5.0102. > Can I propose in a publication that "We attribute these differences to methods for handling bulk solvent in PHENIX that are less adversely affected by deficiencies in the crystallographic data."? > This is a guess, because there is a large contribution to refinement from bulk solvent, rather than factual information. I did cross-refinement, and found it going from structures refined in REfmac to Phenix, and vice versa. The Phenix maps looked better, too. > Is this a reasonable suggestion, and would there be a relevant reference? > Tim > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c> Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c> Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: garib(a)mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk

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