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Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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Visualizing and selecting indivual pockets through pymol #122

Closed dim-99 closed 8 months ago

dim-99 commented 9 months ago

Hi,

I'm trying to calculate volume of a specific pocket using fpocket. After creating the snapshots of my MD trajectory I was able to produce the grid file as per the tutorial (mdpout_freq_grid.dx). To extract the pocket that I'm interested in I used the extractISOPdb.py script.

My question is that when using extractISOPdb.py it produces the output pdb file with all the pockets residue number as 1 which makes it impossible to select specific pockets using pymol. Is there a way to select these pockets one by one even though they all have the same residue number on the PDB?

pschmidtke commented 8 months ago

Hi,

the extractISOPdb script is just a helper script to extract ALL pocket grid points at a given isovalue. The pocket number therein is irrelevant as the pocket sorting is independent for each snapshot when analyzing a full trajectory.

So you'll have to painstakingly select your area of interest by hand.