Well - if you restrict the search to the asymmetric unit, you should
only get one set of peaks (except maybe for pathalogical cases such as
cubic SGs where it is rather hard to restrict to a asymm unit..)
If you search around a molecule you should get peaks near that molecule.
but there may be duplicates where there are close contacts, depending on
the radius you have selected.
Eleanor
Jose M de Pereda wrote:
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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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