Perhaps this could be helpful:
https://bl831.als.lbl.gov/~jamesh/bin_stuff/
In particular the bottom of this page:
https://bl831.als.lbl.gov/~jamesh/bin_stuff/xray_formats.html
The "floatgen" program seems like what you need. If you feed it a stream
of text numbers on stdin it will convert them into 4-byte floats on
stdout. This you would append to a CCP4-type map header in order to make
a CCP4 map file. You can make the header using my make_maphead.com script:
https://bl831.als.lbl.gov/~jamesh/bin_stuff/make_maphead.com
Once you have the cubes in CCP4 format you should be able to use coot to
align the maps after aligning two PDB files corresponding to the
coordinates of interest. Its the "Transform map by LSQ model fit ..."
menu under Map Tools...
Is that helpful at all? (I should really come up with a better name for
bin_stuff.)
-James Holton
MAD Scientist
On 1/17/2025 12:02 AM, Tim Gruene wrote:
Dear Paul, dear everyone,
I need to compare two Gaussian Cube files (Paul Bourke's
page https://paulbourke.net/dataformats/cube/ is the best description I could
find), and my first approach would be a map correlation coefficient at the van
der Waals surface. Does anyone know how to do this?
Details:
The cube files contain the electrostatic potential map of a single
Tyrosine molecule (derived in two different ways). Both files include
the tyrosine coordinates. They are oriented differently. Also the grid
spacing is different, requiring map interpolation.
I would superpose tyrosine A onto tyrosine B and transform map A the
same way to superpose it with map B. Then I would calculate their
mapCC, ideally in certain sub-volumes, and with the possibility to
define the surface as van-der-Waals-surface. I coded something myself,
but I am not sure how long it would take me to debug the code so that I
trust the result.
I did not find a way to read a cube file with coot, and ccp4mg
(from ccp4 8.0, admittedly) crashes with a segmentation fault when
opening either map.
The background:
My PhD student and I think the two maps look quite comparable, given
their different origin, but two reviewers think they do not look alike.
I was hoping for a CC that gives a number to the looks (ideally a
number > 60% ;-))
Best wishes,
Tim
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