Hi Jennifer, ok, I can add this option. Just curious... why you need to format it this way? Also, what is in B-factor column? Pavel. On 7/23/2008 2:26 PM, Jennifer Ekstrom wrote:
Hi Pavel, I'm actually looking for a way to get that peak data into the the format given by cns. I've pasted an example below...
Thanks, Jennifer
......................
REMARK DATE:16-Jan-2008 04:53:47 created by user: ekstrom REMARK VERSION:1.1 ATOM 6706 PEAK PEAK 1 2.936 -26.732 8.585 1.00 12.12 PEAK ATOM 6707 PEAK PEAK 2 -29.892 -17.631 49.107 1.00 11.30 PEAK ATOM 6708 PEAK PEAK 3 -22.298 -14.560 50.705 1.00 9.38 PEAK ATOM 6709 PEAK PEAK 4 -0.284 -37.687 22.843 1.00 8.50 PEAK ATOM 6710 PEAK PEAK 5 -26.184 -10.173 38.207 1.00 8.43 PEAK ATOM 6711 PEAK PEAK 6 -27.455 -11.757 37.651 1.00 7.88 PEAK ATOM 6712 PEAK PEAK 7 0.251 -36.207 17.111 1.00 7.54 PEAK ATOM 6713 PEAK PEAK 8 -36.967 7.877 42.542 1.00 7.44 PEAK ATOM 6714 PEAK PEAK 9 1.491 -38.169 16.878 1.00 7.44 PEAK ATOM 6715 PEAK PEAK 10 -27.501 -10.922 37.959 1.00 7.35 PEAK ATOM 6716 PEAK PEAK 11 4.477 -45.133 14.678 1.00 7.21 PEAK ATOM 6717 PEAK PEAK 12 -0.963 -25.803 18.167 1.00 7.04 PEAK ATOM 6718 PEAK PEAK 13 -26.482 -13.615 36.693 1.00 6.93 PEAK ATOM 6719 PEAK PEAK 14 -26.015 -10.239 30.585 1.00 6.86 PEAK ATOM 6720 PEAK PEAK 15 -30.002 -26.868 20.550 1.00 6.69 PEAK ATOM 6721 PEAK PEAK 16 -27.396 -11.906 38.698 1.00 6.65 PEAK ATOM 6722 PEAK PEAK 17 -31.373 -6.638 28.568 1.00 6.64 PEAK ATOM 6723 PEAK PEAK 18 -8.221 -55.948 9.682 1.00 6.53 PEAK ATOM 6724 PEAK PEAK 19 -28.291 -23.724 37.848 1.00 6.28 PEAK ATOM 6725 PEAK PEAK 20 -30.468 -30.466 41.446 1.00 6.18 PEAK ATOM 6726 PEAK PEAK 21 -31.063 -29.443 40.172 1.00 6.12 PEAK ATOM 6727 PEAK PEAK 22 -26.755 -11.332 32.107 1.00 6.07 PEAK ATOM 6728 PEAK PEAK 23 1.773 -36.238 17.792 1.00 6.05 PEAK ATOM 6729 PEAK PEAK 24 -29.413 -25.920 38.032 1.00 6.04 PEAK ATOM 6730 PEAK PEAK 25 -28.233 -22.681 37.519 1.00 6.03 PEAK ATOM 6731 PEAK PEAK 26 -16.125 -21.401 26.461 1.00 5.99 PEAK ATOM 6732 PEAK PEAK 27 0.732 -34.913 18.222 1.00 5.98 PEAK ATOM 6733 PEAK PEAK 28 -27.046 -9.637 32.604 1.00 5.90 PEAK ATOM 6734 PEAK PEAK 29 -29.019 -24.193 39.115 1.00 5.87 PEAK ATOM 6735 PEAK PEAK 30 2.977 -35.032 16.644 1.00 5.76 PEAK END
Pavel Afonine wrote:
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
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