Hi
This was brought to my attention after I posted yesterday, to add to the list I
sent then -
pyvol - Python (as a PyMol plug-in, a python module and as a command-line
Python script) - needs a config file to run -
https://schlessinger-lab.github.io/pyvol/index.html
The output is the surface of the pocket as vertices and faces in a file with
the extension “.obj” (the other programs fill the pocket with dummy atoms).
Result looks most similar to that from parKVFinder.
Again, many thanks for the input
Harry
> On 12 Jan 2023, at 11:26, Harry Powell <[email protected]> wrote:
>
> Hi folks
>
> a round-up of what I’ve found - four examples that I can run from the
> command-line.
>
> fpocket - mostly C, C++ - https://github.com/Discngine/fpocket
>
> ghecom - C - https://pdbj.org/ghecom/
>
> parKVFinder (replaces KVFinder, also available as a Python module) - Python:C
> 60:40 - https://github.com/lbc-lnbio/parkvfinder
>
> p2rank - Groovy, Java (won't run with Java 19 on my High Sierra box, works
> with Java 17) - https://github.com/rdk/p2rank
>
> and some screenshots (from QtMG) of the surface of the largest pocket found
> by each (using default settings) for the polypeptide from chain A of 1A9W (a
> haemoglobin) I’ve removed all HETATMs from this before running the progs)
> superimposed over the haem (or heme, if you prefer ;-)) - in the order of the
> programs given above -
>
> <fpocket_33.png><fpocket2_33.png>
> <ghecom_33.png><ghecom2_33.png><kvfinder_33.png><kvfinder2_33.png><p2rank_33.png><p2rank2_33.png>
> Harry
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