Hi,
I would run HOLE, which detects the tunnel/channel and generates a file
for you (SPH?) which is a pdb file with SPH (sphere) atoms corresponding
to the tunnel/channel volume.
You can select water molecules (or anything else) around these SPH atoms.
Suggestion: the ends of the tunnel are broadening with a lot of spheres;
you most likely want to remove those SHP atoms...
Bests,
Tamas
On 3/19/21 6:31 PM, Jason Mosier wrote:
Hello, I was wondering if someone could help me screen for which
molecules are being found within the inside of a protein channel /
near the protein channel. I know I can search for the molecules within
3.5 A of the protein, but this also results in finding the ones on the
outside. I know this is pretty specific and might be difficult to do,
but it would increase our accuracy a bunch because at the moment we
are hand picking which water molecules "seem" to be close to the
channel and our numbers are very inconsistent. Here is the current
code we are using: https://pastebin.com/1iBZ7rKi
<https://signaldomn.online/click?redirect=https%3A%2F%2Fpastebin.com%2F1iBZ7rKi&dID=1616175096424&linkName=https://pastebin.com/1iBZ7rKi>
Best,
Jason M.
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
