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

[Peter Zwart]

Hi Partha,

> 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

Loose the ' < '


> 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?

I must confess that I think that the phenix.refine interface is as
easy as it gets and is a much better option than tradiaionl input
files. If you have the feeling that the parameter file is too
overwhelming in terms of number of parameters, just loose the scopes
and parameters you are not interested in: default values will be used
in those cases.

If you really want to go for keyword based input as is done in
SOLVE/RESOLVE , I recommend you  read the newsletter
http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf
on the PHIL parameter file.


> 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?

Just read in the a cif file like this

phenix.refine m.mtz m.pdb tpo.cif

or like this

phenix.refine m.def tpo.cif

or add it in the parameter file in the appropriate scope.

HTH

P

> Best, Partha
>
>
>
>
> 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
> >
> > 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>:
> > > 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
> > > Phone: + 44 208 816 2515
> > > _______________________________________________
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> > >
> > >
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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
> Phone: + 44 208 816 2515
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