On 31/12/2019 14:22, Sruthi Unni wrote:
This post is regarding Mogul for checking the ligand geometry. The Mogul stats
generated in COOT didn't show any flags for our ligand in protein-complex file but our PDB validation did show.
That, a priori, seems unlikely to me (given that Mogul was correctly executed
when started from Coot).
Based on our search, we could find Mogul linked with Coot in the back end with options to : 1) calculate the
tabulation of the geometries in Mogul output on the coot terminal ; and 2) Show the ligand distortions.
I wrote the interface to Mogul from Coot at a time when I thought it would be important and ubiquitous - and
that was a while ago. I don't recall those functions being wrapped around the Mogul output. I think rather
they refer to the ligand dictionary.
But,
we could not find any link to download and run an _independent plugin_ or _downloadable software_ or any
_independent web server_ to run Mogul and check the ligand stats of my PDB file.
Well, the API is tailored for the full ligand test, not just the Mogul validation. But I think that this
will work if you have mogul available in the shell from which you started coot:
Calculate -> Scripting -> Scheme...
(run-mogul-show-results imol res-name 'bonds-and-angles chain-id res-no
ins-code)
You will need to provide values for imol res-name chain-id res-no and ins-code
of course.
(I haven't tested this.)
If you change your ligand be sure to remove the Mogul *.out file otherwise Coot will use that for the
results instead of running Mogul again.
Paul.
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