- phenixbb - phenix-online.org

Re: [phenixbb] CCI apps bundles upgrading
by Ralf W. Grosse-Kunstleve 20 Dec '06

20 Dec '06

Hi Miguel, Thanks for asking the question! I just added this information to the CCI Apps download page: Please do NOT install CCI Apps inside an existing Phenix installation. It is best to install the CCI Apps bundle in a new, separate, empty directory. To override the Phenix commands with more recent equivalents in CCI Apps (e.g. phenix.refine), source cci_apps_build/setpaths.csh AFTER source phenix_env. Sorry for not explaining this earlier. It is just one of the things we don't usually think about as developers. Please let us know if there are other issues like this. Cheers, Ralf

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CCI apps bundles upgrading
by Miguel Ortiz Lombardia 20 Dec '06

20 Dec '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, This is a pretty newbie question. I have phenix installed at: /usr/local/phenix-1.24.1b and have downloaded the new version of the CCI Apps. I would like to install/upgrade them in my current installation (I have a backup, of course ;-) Should I simply run: python /PATH-TO/cctbx_sources/libtbx/configure.py phenix in the /usr/local/phenix-1.24.1b directory and then do the: source setpaths.csh libtbx.scons or it should be done differently to keep the phenix installation working? Thank you! Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFFiVtPF6oOrDvhbQIRAkcKAJ414Qrsa+8DSj67uFQ6gv56Sc7TRQCfY8xG 7jXKhu+xv6nCc90xYjXt0T8= =2vZq -----END PGP SIGNATURE-----

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Anisotropic ADP
by James Fraser 16 Dec '06

16 Dec '06

Hello, We've just started using phenix.refine and I'm a bit confused about whether anisotropic ADP's are actually being used or not. On the wiki (http://www.phenix-online.org/phenix_wiki/phenix.refine) it says: << phenix.refine is the macromolecular refinement engine of the Phenix suite. It features * Individual as well as grouped B factor refinement * Anisotropic or isotropic+anisotropic B factor refinement * TLS refinement >> However, the documentation says (http://www.phenix-online.org/download/documentation/phenix/phenix/structure…): << Current limitations * No restrained individual anisotropic ADP refinement >> In my .def file I can set: adp { individual { isotropic = None anisotropic = chain a force_all_to_be_refined_isotropically = True } and get ANISO lines in my output pdb. But I'm confused as to whether this is actually refining with individual anisotropic b's for chain a (analagous to refining with anisotropic temperature factors in refmac). Should I be resetting the force_all... to false? Can someone with more knowledge clarify this? Thanks, the program seems to be working great otherwise! James Alber Lab UC Berkeley

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Re: [phenixbb] questions / TLS+NCS bug
by Pavel Afonine 15 Dec '06

15 Dec '06

Hi Jianghai, Thanks for the .log file ! I looked at it and now I think I now what's the problem: this is the bug in phenix.refine that we will fix for the next release. The bug arises when you try to refine using TLS and NCS at once. Sorry for this. The possible solution is to split your refinement into 2 parts: 1) First, refine coordinates and isotropic B-factors. Use NCS restraints. DO NOT refine TLS. 2) At the end, as the final tune up, refine ONLY isotropic B-factors + TLS and do not refine coordinates. For this run, please REMOVE all NCS information (NCS selections) from the command file. This refinement run should be the final one. Once again, sorry for the inconvenience. This will be fixed in the next release of CCI APPS and PHENIX. Once this fixed, you will be able to run everything in "one go" and in any combination. Please let me know if what I suggested helped you. Any further questions are welcome! Cheers, Pavel. Jianghai Zhu wrote: > Here is the log file. Thanks. > > Jianghai > > = > ------------------------------------------------------------------------ > > > > On Dec 14, 2006, at 12:50 PM, Pavel Afonine wrote: > >> Hi Jianghai, >> >> could you please send us .log file from your refinement run, so we >> can analyze what's going on. >> >> In general, "bad" B-factors can be: >> - misplaced model; >> - inadequate TLS model (= domains chosen for TLS do not correspond to >> the reality). >> >> If you are using like 2 months old or older version of phenix.refine, >> you may want to get the latest CCI APPS since we made lots of >> improvements. Just goto http://www.phenix-online.org/download/cci_apps/ >> >> Pavel. >> >> >> Jianghai Zhu wrote: >>> The resolution is 2.5 A. The wilson B is about 50. I know B factor >>> of the backbone is lower than that of the sidechian. But a B factor >>> like 4 is definitely wrong. >>> >>> Jianghai >>> >>> >>> On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote: >>> >>>> >>>>>> 4) The refinement (TLS + ML + B individual) went through, I got >>>>>> reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are >>>>>> pretty low. The B factor of the backbone is much lower than the >>>>>> side >>>>>> chain, some have numbers like 4. Some metal atoms also have B >>>>>> factors around 4. What did I do wrong? >>>> >>>> What is the resolution of your data? >>>> >>>> Backbone B-s usually are lower than the main chain. >>>> >>>> What is the Wilson B value reported by phenix.refine? >>>> You could re-refine and randomize all B-values and see what happens (I >>>> have to get back to you to to get the exact command for this). >>>> Maybe it >>>> is useful to obtain a copy of the latest verison of phenix.refine by >>>> downloading cci_apps from our server http://www.phenix-online.org. >>>> >>>> >>>> If your B-values still come out lowish, try growing crystals that >>>> do not >>>> diffract very well, that usually does the trick. >>>> >>>> HTH >>>> >>>> Peter >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> ------------------------------------------------------------------------ >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > =

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Re: [phenixbb] questions
by Ralf W. Grosse-Kunstleve 14 Dec '06

14 Dec '06

> 3) When I ran phenix.refine, I found the following message in the log. > > Number of residues, atoms: 32, 418 > Unusual residues: {'NAG': 22, 'MAN': 10} > Classifications: {'undetermined': 32} "Unusual" means "not peptide, rna/dna, or water". It is just for information. If phenix.refine cannot find matching CIF restraint definitions, it will report "Unknown residues". Ralf

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NCS in phenix.refine
by Alessandro S. Nascimento 13 Dec '06

13 Dec '06

Hi all, I've searched in phenix manuals but I didn't find how to deal with ncs in parameter file. Also, how to prepare simulated annealing keeping ncs restraints? Is it already possible in 1.24b version? Any idea? thanks, - alessandro

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Maybe a bug?
by Zhongli Cui 22 Nov '06

22 Nov '06

Phenix is a quite useful suite in solving protein structure. But I met a problem during running phenix1.24.1b on a suse 10.1 environment. When I try to load pdb file from the window, the phenix GUI will close automatically. But it runs OK, if I input the file name manually into the window.

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refining a twin
by Bryan W. Lepore 21 Nov '06

21 Nov '06

i see there are map utilities for twinned data. but before i go try refinement of a twin - will phenix.refine refine against twinned data? if so, is alpha determined each time, thus, alpha is not specified in the .def? -bryan

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HA clusters
by Morten Grøftehauge 14 Nov '06

14 Nov '06

Hi, This is probably a stupid question but how do I tell AutoSol to look for a heavy-atom cluster rather than individual atoms? Or should I just find the cluster as a superatom in CNS and input the refined co-ordinates? Thanks, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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fixing atoms during refinement
by Gregers Andersen 02 Nov '06

02 Nov '06

Is there anyway through selection to fix selected atoms during minimisation/sim annealing in phenix.refine? Gregers Rom Andersen Associate Professor, Ph.D. Dep. Molecular Biology Gustav Wiedsvej 10C DK8000 Aarhus C Denmark phone +4589425024 fax +4586123178 <http://www.bioxray.dk/research_gra_uk.php> http://www.bioxray.dk/research_gra_uk.php Please notice new email: <mailto:[email protected]> gra(a)mb.au.dk

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