Hi all !! Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement. regards John
Hi John, no. This was done many years ago in XPLOR, but programs such as phenix.refine, CNS and refmac do not use charges. Their inclusion tends to generate problems (incorrectly placed residues being strongly attracted to one another). In the future we hope to investigate methods to use charges towards the end of refinement. Cheers Paul On Aug 1, 2007, at 10:11 AM, john kryst wrote:
Hi all !!
Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement.
regards John _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Hi all and Pavel !!
I asked this question more of academic interest than for any
particular purpose. Thanks a lot.
regards
John
On 8/1/07, Paul D. Adams
Hi John,
no. This was done many years ago in XPLOR, but programs such as phenix.refine, CNS and refmac do not use charges. Their inclusion tends to generate problems (incorrectly placed residues being strongly attracted to one another). In the future we hope to investigate methods to use charges towards the end of refinement.
Cheers Paul
On Aug 1, 2007, at 10:11 AM, john kryst wrote:
Hi all !!
Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement.
regards John _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center
Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/
Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi, we don't have it in refinement. However you are not the first one who asked about this and I'm aware of strong motivations of using them for certain purposes, so I'm really interested to know why you need it. At the moment I'm collecting the information from different sources to see what we can do or try to do in future. Thanks! Pavel. john kryst wrote:
Hi all !!
Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement.
regards John ------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Pavel, My indexing routine found a few typos; I think these are coming from all the nice new phenix.refine documentation that you have added! A few may also be from other places, including xtriage. All the best, -Tom T actualy anirotropic anomaluos anomaluous ansiotropic anylysis assignement cartesisan comparisions componet comprihensive cutted developper diviations documnetation fourrier friquently gradially groupped lenghts maipulations manipulatons negligeable presenrted refineemnt refinemet reifne responsability restarints stattistics unchanched
Hi Tom, thanks for findings! I will check for this. I also hope someone (native speaker) reads it before the release to make sure it's actually written in English and not in "Russian English" -:) Thanks again! Pavel. Thomas C. Terwilliger wrote:
Hi Pavel,
My indexing routine found a few typos; I think these are coming from all the nice new phenix.refine documentation that you have added! A few may also be from other places, including xtriage. All the best,
-Tom T
actualy anirotropic anomaluos anomaluous ansiotropic anylysis assignement cartesisan comparisions componet comprihensive cutted developper diviations documnetation fourrier friquently gradially groupped lenghts maipulations manipulatons negligeable presenrted refineemnt refinemet reifne responsability restarints stattistics unchanched _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (5)
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john kryst
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Paul D. Adams
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Pavel Afonine
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Peter Zwart
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Thomas C. Terwilliger