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jr-marchand / caviar

// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition
https://jr-marchand.github.io/caviar
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Pharmacophore type and buriedness in *_subcavs.pdb output file #9

Open piermichele-kobauri opened 2 years ago

piermichele-kobauri commented 2 years ago

First of all, thank you very much for this super helpful tool, great work!

When I run from the command line: caviar -code 3DAU -chain_id A -out ~/

after inspecting the generated files, it seems to me that only the 3DAU_cavs.pdb file contains pharmacophore type and buriedness as occupancy and temperature factor.

Is there a way to keep such information also in the 3DAU_subcavs.pdb file?

Many thanks in advance!

jr-marchand commented 2 years ago

Hi Piermichele,

Good point, you are right! This information is only present in the cavities file, not in the subcavities one. I haven't realized that before. I'll try to get this sorted in a few days and will ping you when it's done. If you need it urgently, you can easily grep/replace the information from _cavities.pdb to _subcavs.pdb as the grid points have the exact same coordinates. Thanks a lot for the kind words, this is really motivating!

Cheers, JR

piermichele-kobauri commented 2 years ago

Hi JR,

Awesome, looking forward to your fix, thank you! I also have another question/suggestion related to the subcavity search output. Do you think it would be possible to print the list of residues that form each subcavity?

All the best, Piermichele