jr-marchand / caviar Goto Github PK

This is a naive question - but does Caviar rely on any of the chemical properties of the protein/biomolecule? Or is it just element and coordinates that are important to the calculation? I would be interested in using something like this on structures I have generated that have PDB files.

Hi,

Thanks for writing this package. I have read your paper and I am very impressed by the results you have shown.
I have tried to install Caviar on my Mac to do some testing. I have come across the following bug. Any suggestions on how to resolve this is would be highly appreciated.

I am using python 3.7.8 and the OS is macos catalina verson 10.15.6

Traceback (most recent call last):
  File "/Users/leeladodda/anaconda3/envs/caviar/bin/caviar", line 33, in <module>
    sys.exit(load_entry_point('caviar==1.1.0', 'console_scripts', 'caviar')())
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/pkg_resources/__init__.py", line 488, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2872, in load_entry_point
    return ep.load()
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2472, in load
    return self.resolve()
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2478, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/caviar/caviar.py", line 7, in <module>
    from caviar.prody_parser import *
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/caviar/prody_parser/__init__.py", line 73, in <module>
    from . import kdtree
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/caviar/prody_parser/kdtree/__init__.py", line 5, in <module>
    from .kdtree import KDTree
  File "/Users/leeladodda/anaconda3/envs/caviar/lib/python3.7/site-packages/caviar/prody_parser/kdtree/kdtree.py", line 18, in <module>
    from ._CKDTree import KDTree as _KDTree
ModuleNotFoundError: No module named 'caviar.prody_parser.kdtree._CKDTree'

Thanks for making the code available and great work.

Best wishes,
Leela

Setting a zero/very low threshold for trim_score ends up in faulty behavior/exclusion of all cavities. Doesn't make sense. Only in case of modifications of radius_cube and min_burial!!

Request via email:

Focus the cavity analysis only on certain residue(s) or on a centroid [x,y,z].

Easy hack, but needs a few more options and documentation:

• restrict the post-processing to cavities with the user-defined residues
• generate the search box around a user-defined (x,y,z) and size instead of automatically setting it at the center of the PDB

If a PDB is truncated and does not have the element column (column 77-78 of the PDB format), the function "find_protein_points_variablevolumn" in cavitydetect.py glitches.

It doesn't find any atom of the protein and prints out "CAVIAR does not find a cavity".

The selection tool in this function is based on element, there may be a work around with a selection based on atom "name".

For some reason, the link to PyMOL crashes in the caviar_gui, under OSX.
Might be good to investigate it at some point.

All of the cavities residues data is stored in memory for clustering at the end of MD frames parsing. CAVIAR ends up running out of RAM if > 100 frames (depends on the number of cavities/size of the system).

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!

Hello,

This software is great! It is fast and does precisely what I want it to do. I am interested in using it for analyzing voids and cavities in molecular dynamics simulations (PDB files with many conformers, similar to NMR structures) but with an initial attempt, it seems to only calculate the cavities for the first PDB structure. I understand this would take multiplicatively longer to process the number of frames, but this would be quite useful!

Regards,
Jacob