Dear Murpholino,
I did not reply earlier because I thought there were plenty of solutions.
In case it helps, you can get peaks from the difference map with the program
'knuspr' using e.g. the following input script:
-----> 1id3_diff.in <-------------
data_mtz 1id3-sf_refmac1.mtz
mtz_path "*/*/[DELFWT PHDELWT]"
ebody_pdb 1ID3-ebodies.pdb
maxima_pdb maxima.pdb
MAP_MAXIMA_CUTOFF 2.5
MAP_MAXIMA_DMIN 2.3
-----> 1id3_diff.in <-------------
and run knuspr with
#> knuspr -i 1id3_diff.in
You probably want to stop the program after 2-3s (which it might take to find
the peaks and write maxima.pdb). knuspr would continue placing bases and
phosphates at it was originally written for autotracing nucleic acids.
The file 1ID3-ebodies.pdb contains refined peaks (blobs) as described in
(http://dx.doi.org/10.1107/S0108767310039140)
If you think this is useful for you, I could add a keyword to interrupt knuspr
after the maxima were found.
Cheers,
Tim
On Friday, October 23, 2015 10:32:34 PM Paul Emsley wrote:
> On 14/10/2015 16:29, Murpholino Peligro wrote:
> > Is there a way to load a pdb and a difference map (ccp4 format) in
> > coot, with a bash script, and then get the "validate->difference map
> > peak" analysis?
> >
> >
> > I was thinking in doing a small script in bash, because I am doing it
> > manually and there are a lot of pdbs and maps to check...
>
> There is no API which returns the results (as there should be) but you
> can run coot in a script that loads the map and model and calls the
> function difference-map-peaks. You will then have to "grep" the log
> file looking for lines that contain "xyz = " after " Found these peak
> positions:"
>
> Hideous, but it should work.
>
> Paul.
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Dr. Tim Gruene
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