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@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@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@nimr.mrc.ac.uk
> Phone: + 44 208 816 2515
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://www.phenix-online.org/mailman/listinfo/phenixbb



--
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra@nimr.mrc.ac.uk
Phone: + 44 208 816 2515