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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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Can I use fpocket to generate cavity spheres? #111

Closed DipeshSomvanshi closed 8 months ago

DipeshSomvanshi commented 11 months ago

Hello. I have played around with fpocket quite a bit, and could not figure out how to create cavity spheres.

The cavity spheres generated have the same radius. I expect the cavity sphere to fill up all the available space between 4 water molecules.

Also, there are many spaces where there should be a cavity, but the cavity sphere is missing. Also, there are many spaces where there are extra cavity spheres.

This is the command I used:

fpocket -m 0.1 -M 10.0 -f water_100_box_10_in.pdb

I think I might be using the wrong command. Can you please help me?

water_test.zip

pschmidtke commented 8 months ago

You have that information in the _pockets.pqr file. The radii are in the B-factor column. For instance for PDB structure 6cs2 you'd get something like that: 

ATOM      1    O STP     1     180.586 154.925 186.892    0.00     3.42
ATOM      2    C STP     1     180.655 155.077 186.963    0.00     3.47
ATOM      3    O STP     1     180.244 154.871 186.966    0.00     3.54
ATOM      4    O STP     1     180.433 155.027 186.965    0.00     3.54
ATOM      5    C STP     1     177.346 156.643 183.611    0.00     3.43
ATOM      6    O STP     1     177.652 156.709 183.709    0.00     3.54
ATOM      7    C STP     1     176.737 155.876 183.768    0.00     3.46
ATOM      8    O STP     1     177.815 156.507 183.894    0.00     3.64
ATOM      9    O STP     1     178.265 156.786 184.693    0.00     3.53
ATOM     10    C STP     1     177.414 156.071 183.959    0.00     3.58
ATOM     11    C STP     1     177.563 156.041 184.623    0.00     3.41
ATOM     12    C STP     1     177.786 156.272 184.012    0.00     3.68
ATOM     13    C STP     1     178.031 156.322 184.527    0.00     3.61
ATOM     14    C STP     1     179.185 155.199 187.066    0.00     3.41
ATOM     15    O STP     1     178.500 156.914 184.925    0.00     3.47
ATOM     16    C STP     1     180.637 155.139 186.999    0.00     3.51
ATOM     17    C STP     1     180.535 155.096 186.989    0.00     3.53
ATOM     18    C STP     1     178.837 156.091 185.454    0.00     3.44

This should be what you are looking for.