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 <[email protected]> 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 < [email protected]>:
> 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
>
>
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> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
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> Phone: + 44 208 816 2515
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>
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