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Dear all,
Related with the peak search in maps I have a question about the output
of symmetry related peaks.
As far as I can tell the peak search done both via the GUI (peakmax) and
by COOT outputs symmetry related peaks. Of course some of the peaks fall
far from the coordinates in the reference PDB file, even if FFT is told
to create the map around atoms in a PDB file. Interestingly the
"Difference Map Peak Analysis" window in COOT has a "Select Model"
option, but it does not seem to restrict the peak search around those
coordinates.
Is there any easy way to get ONLY the peaks near a reference PDB
coordinates and not their symmetry mates?
Thanks
Jose
Eleanor Dodson wrote:
From the GUI forthe FFT click the option - output peaks.
You will get them both in PDB and ha format. You can also ask for both
negative and positive peaks.
Alternately in the COOT validate menu - search for diff map peaks.. -
you can then click through the list..
Eleanor
Donnie Berkholz wrote:
Hi all,
I recently started using CCP4 instead of CNS, but I can't figure out how
to duplicate one of the more useful features. When creating an Fo-Fc
map, CNS also creates two files, e.g. fofc_model_map_negative.peaks and
fofc_model_map_positive.peaks, containing the coordinates and heights of
the largest peaks on the difference map. It's in PDB format and can
essentially be treated as another PDB to be loaded into O or Coot.
I've tried searching the CCP4 documentation, Google and through the
CCP4i, but I just couldn't figure out how to do the same thing in CCP4.
Alternately, an equivalent feature that allows me to navigate through
the locations of the highest peaks in Coot would do just as well.
Thanks for your help,
Donnie Berkholz
--
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Jose M de Pereda, PhD
Centro de Investigación del Cáncer
University of Salamanca-CSIC
Campus Unamuno s/n
E-37007 Salamanca, Spain
Phone: +34-923-294819
Fax: +34-923-294795
http://xtal.cicancer.org/
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