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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> phenixbb at phenix-online.org
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>
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