On 24/11/2021 18:22, Artem Evdokimov wrote:
Thank you Paul
And many thanks to several kind folks who answered privately!
It is always exciting to hear from the coot-master himself :)
Sounds like I may have to cheat the graphics somehow or use pymol or
raster3d.
Artem
On Wed, Nov 24, 2021, 10:01 AM Paul Emsley <[email protected]
<mailto:[email protected]>> wrote:
On 23/11/2021 20:03, Artem Evdokimov wrote:
> Dear Cooters!
>
> I am new to this list, but would love to get a little bit of help
> scripting Coot to do something for me, like this:
>
> 1. read one PDB and one MTZ file
> 2. center on a particular location (ideally defined as e.g. a
residue)
> 3. orient in a particular way (defined as a matrix or however
convenient)
> 4. contour a map (difference or other) at a particular level
> 5. output a snapshot
>
> (all of this without invoking graphical output as such because I
need
> this to happen a few hundred times, for a few hundred PDB-MTZ pairs.
>
> Is it doable?
I think so.
> Could someone recommend at least a barebones script for this?
Do this interactively for one case and then save the state. Then
look at
0-coot.state.py <http://0-coot.state.py> or 0-coot.state.scm. That
should give you some clues.
As for the graphical output screenshot, I have not worked out how
to do
that without invoking X11, so the alternative is to use raster3d.
There
are some parameters to tweak the raster3d representation if you don't
like the default.
The python interface to raster3d:
raster3d("raster3d-example-ligand.r3d")
Then (after) in the shell, run
$ render < raster3d-example-ligand.r3d > raster3d-example-ligand.png
Obviously if you have 100s of them you'd given them different files
names and batch translate them in a script.
Alternatively,
raster_screen_shot()
will run raster3d/render for you and produce "coot.png"
You will then need to use your python file-system functions skills to
rename that to something meaningful.
(Ethan Merritt is the author of Raster3D.)
Paul.
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