Hi Jennifer,

phenix.refine reports the list of highest peaks and deepest holes found at difference map. Look towards the end of .log file for lines like this:

========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                          

Number of peaks found at mFobs-DFmodel map (map cutoff=3.50 sigma)= 21         
Filter by distance & map next to the model:
   mapped sites are within: 1.002 - 3.227
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 20 from: 21
   mapped sites are within: 1.002 - 3.227

peak=    4.154 closest distance to pdb=" N   VAL     2 " =    2.881
peak=    3.572 closest distance to pdb=" O   VAL     2 " =    2.663
peak=    3.895 closest distance to pdb=" CB  ARG     5 " =    2.743
peak=    4.186 closest distance to pdb=" N   GLU     7 " =    2.237
peak=    4.958 closest distance to pdb=" OE1 GLU     7 " =    2.920

Same for negative peaks.

Please let us know if you have any questions!

Pavel.
 


On 7/23/2008 1:22 PM, Jennifer Ekstrom wrote: 
I would like to obtain a file with a listing of positive and negative 
difference map peaks, similar in formatting and content to the files 
that would come out of cns: 

         positive peaks in: <output_root>_positive.peaks
         negative peaks in: <output_root>_negative.peaks


We need this for use in DDQ at the jcsg validation server 
(http://www.jcsg.org/prod/scripts/validation/sv2.cgi).  Is there an easy 
way to create these peak files in phenix.refine?  We'd prefer to not 
re-refine in CNS as we have *many* alternate conformations... 

Thanks, Jennifer
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