[phenixbb] Request for C shell script file for phenix.refine
ppchak at gmail.com
Mon Oct 1 05:59:40 PDT 2007
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?
On 9/28/07, Peter Zwart <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
> 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.
> 2007/9/28, Partha Chakrabarti <ppchak at gmail.com>:
> > Hi,
> > I am wondering if one can have master scripts (C shell) for the macro
> > 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
> > 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
> > Phone: + 44 208 816 2515
> > _______________________________________________
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> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
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> phenixbb at phenix-online.org
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra at nimr.mrc.ac.uk
Phone: + 44 208 816 2515
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