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

Peter Zwart PHZwart at lbl.gov
Fri Sep 28 11:59:43 PDT 2007

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 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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