[phenixbb] How to use the STIR command in phenix.refine?

Pavel Afonine PAfonine at lbl.gov
Thu Mar 13 13:00:19 PDT 2008

Hi Nick,

I temporarily disabled this option since I've never seen it useful 
within phenix.refine context. Why don't you use the whole resolution 
range for the refinement? It should work just fine.

Also, doing high resolution refinement in phenix.refine please review 
"Refinement at high resolution" paragraph of phenix.refine manual 

Please let me know if you have any other questions!

On 3/13/2008 12:42 PM, nick at silvaggi.com wrote:
> Hello,
> I am refining a high-resolution X-ray structure and I would like to  
> gradually increase the resolution from 1.5 to 1.0A, as I used to do in  
> shelxl. I know the STIR command is the way to do this, but I cannot  
> figure out the syntax to use. Currently I am using the following  
> commands:
> high_resolution = 1.0
> low_resolution = None
> stir = 1.5
> When I run phenix.refine (2008_02_08_1610) it echos a line that says  
> "STIR 1.5" before the first macrocycle, but at each stage I see  
> "(resolution: 1.00 - 21.77)." Obviously I am not using the STIR  
> command correctly. Any advice would be greatly appreciated.  Thanks in  
> advance.
> Nick Silvaggi
> Department of Physiology and Biophysics
> Boston University School of Medicine
> 715 Albany St. R-702
> Boston, MA 02118
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