[phenixbb] Request for C shell script file for phenix.refine

[Nigel W. Moriarty]

Partha

Modified residues can be handled by eLBOW.  Run

phenix.elbow file.pdb --do-all --opt

to get a CIF file to pass to phenix.elbow.  The option --opt is optional 
but recommended.

Nigel

On 10/1/2007 5:59 AM, Partha Chakrabarti wrote:
> Hi Peter,
>
> Thanks a lot for your suggestions. Its close but not completely happy yet.
> So, I generated the file as you suggested, several of the commands are 
> understandable, and I can run it after modification as:
>
> $ phenix.refine <parameter.def
>
> but would be easier if there is a scrip for phenix.refine as available 
> for SOLVE/RESOLVE. Could you point me to the not so easy way of doing 
> that?
>
> One particular problem seems to be modified residues, in my case, a 
> phosphothr (TPO), had to delete the phosphate and rename TPO as THR.. 
> is there any wayout?
>
> Best, Partha
>
>
>
> On 9/28/07, *Peter Zwart* <PHZwart at lbl.gov <mailto:PHZwart at lbl.gov>> 
> wrote:
>
>     The easiest way is to have a parameter file that you edit.
>     The easiest way to get a parameter file is by typing
>
>     phenix.refine <model> <data> --dry_run
>
>     and use the subsequently generated ???_refine_001.eff file.
>
>     rename that eff file to something like
>
>     parameters.def
>
>     which you can use for subsequent customisations and editing of
>     parameters.
>
>     Not ethat every time you finish a refinement job, a new def file is
>     generated of rthe next round, updating the model info for further
>     rounds of refinement.
>
>
>     P
>
>
>
>
>
>
>
>
>
>
>
>
>
>     2007/9/28, Partha Chakrabarti < ppchak at gmail.com
>     <mailto:ppchak at gmail.com>>:
>     > Hi,
>     >
>     > I am wondering if one can have master scripts (C shell) for the
>     macro cycle
>     > of phenix.refine that can be used from the command line. It is
>     easier to
>     > comment out an option than having to type the whole thing.. has
>     anybody
>     > tried it? Similar scripts exist for solve/resolve and phaser..
>     >
>     > I should not say it, I am myself not adverse to using the GUI,
>     it is just
>     > easier when the poor postdoc sits with the boss.. typically I
>     face the
>     > question: where is the script file & where is the log file :))
>     >
>     > Cheers, Partha
>     >
>     >
>     > --
>     > MRC National Institute for Medical Research
>     > Division of Molecular Structure
>     > The Ridgeway, NW7 1AA, UK
>     > Email: pchakra at nimr.mrc.ac.uk <mailto:pchakra at nimr.mrc.ac.uk>
>     > Phone: + 44 208 816 2515
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>
>
> -- 
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pchakra at nimr.mrc.ac.uk <mailto:pchakra at nimr.mrc.ac.uk>
> Phone: + 44 208 816 2515
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov

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