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:
_positive.peaks negative peaks in: _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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb