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Hi Jennifer,<br>
<br>
ok, I can add this option.<br>
<br>
Just curious... why you need to format it this way? Also, what is in
B-factor column?<br>
<br>
Pavel.<br>
<br>
<br>
On 7/23/2008 2:26 PM, Jennifer Ekstrom wrote:
<blockquote cite="mid:4887A217.8080600@msu.edu" type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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
(<a class="moz-txt-link-freetext" href="http://www.jcsg.org/prod/scripts/validation/sv2.cgi">http://www.jcsg.org/prod/scripts/validation/sv2.cgi</a>). 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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