[phenixbb] Command to call/read external file when running phenix.refine from

Kendall Nettles knettles at scripps.edu
Fri Oct 23 07:19:25 PDT 2009

Hi Ashley,
Perhaps you could input a second parameter file with the additional restraints into the command line? Or make a single run file to invoke phenix.refine with your inputs and parameters?
Best regards,
Kendall Nettles

On 10/23/09 9:31 AM, "Ashley Pike" <Ashley.Pike at sgc.ox.ac.uk> wrote:

I am running phenix.refine(v.1.5.2)  from the command line using a batch file containing all my customised options ie. phenix.refine my_parameters. From this batch file (my_parameters) I also want to include additional geometric and NCS restraints. Rather than have them clutter things up, I want to call/invoke them from an external file instead. I had been told that this is possible using the command 'include file <filename>' but it seems that this is not doing what I had hoped. When run in this way phenix.refine doesn't complain but is not using the restraints. Needless to say everything is fine when I actually include the information directly in the batch file. Any hints what I am doing wrong?



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