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

Nathaniel Echols NEchols at lbl.gov
Fri Oct 23 06:37:19 PDT 2009

On Oct 23, 2009, at 6:31 AM, Ashley Pike 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?

What happens when you simply pass all of the parameter files as  
command-line arguments?  It should parse all of them and combine the  

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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