VMD plugin and cli output different pocket volumes

[ParkerdeWaal]

Hello Epock developers,

While using the following epock configuration file I obtain two completely different volumes between the VMD plugin and the standalone executable on the same PDB file (1331.00 vs 857.75).

[DEFAULT]
grid_spacing = 0.4
contiguous = true
contiguous_cutoff = 2.0

[pock1]
include_sphere         =    36.05    35.58    64.60  9.0
contiguous_seed_sphere =    36.05    35.58    64.60  5.0

Attached to this email is a partial PDB file of the cavity which can be used to replicate this inconsistency. Maybe it's possible I'm missing a critical setting for the CLI executable that is taken for granted in the VMD plugin?

Cheers, Parker

[Benoist LAURENT]

Hi Parker,

Thanks for using Epock and for your feedback.

By loading your configuration file in Epock VMD plugin, I noticed that the Contiguous opt. setting wasn't set adequately (was false while it should have been true according to your configuration file).

Therefore, Epock calculated without removing non-contiguous points, leading to a different and higher volume.

Thanks a lot for reporting that. This behaviour is clearly a bug and will fixed soon.

Cheers, Ben