So I was trying to get the pockets in a protein PDB file. I uploaded my PDB file to CASTp website ( http://sts.bioe.uic.edu/castp/calculation.php ) and got necessary information. Pymol has a CASTp plugin. But I use VMD to visualize the PDB files etc. Can I visualize the .poc file generated by CASTp in VMD ? .poc file is similar to PDB file with a difference of having pocket number left to segname. I don't have any idea how to access this number. My basic aim is to call this POCKET number like "resname" as in VMD.
I am attaching a screenshot of .poc file
1. Make a list of atom identifiers belonging to each pocket.
2. In VMD, create a selection for each pocket using "index" command.
---
# 1. python
D = {}
for line in open("filename.poc"):
atid = line.split()[1] # atom id
pid = line.split()[-2] # pocket id
if pid not in D:
D[pid] = []
D[pid].append(atid)
pockets = [pid for pid in D]
pockets.sort()
for pid in pockets:
print(pid, " ".join(D[pid]))
You can directly open the poc file (with pocinfo file, generated by CASTp) from Chimera, then you'll see each pocket on protein structure
On what basis I can chose some selective pocket ID from CAST-P results.Is there any rule to chose 3 to 5 pockets only from the Pocket ID lists ?
- Badges
- Science topic
- Similar topics
- Linguistics
- Composition Studies
- Writing