Thank you again :)
Artem
- Cosmic Cats approve of this message
On Wed, Nov 24, 2021 at 5:27 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:
>
> 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 <pems...@mrc-lmb.cam.ac.uk>
> 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 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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