How I can merge 2 pdb files correctly on pyMol
1
0
Entering edit mode
4 weeks ago
hajar94 • 0

Hi there,

Please, I'm not experienced in this field and I need help. I want to check the ligand-interaction of 2 molecules, but I'm not able to merge the 2 PDB files correctly, because it's like the ligand is not in contact with the protein at the right site as it was shown in the literature. There is another problem, I can only find the molecule (that is supposed to be a ligand) as a protein on PDB, there is any way to convert it to a ligand PDB file?

Thank you in advance.

ligand-interaction file pdb merge • 145 views
ADD COMMENT
0
Entering edit mode
4 weeks ago
Mensur Dlakic ★ 14k

I think there are many things in your post that require clarification if you are expecting meaningful answers, but I will give it a try.

First, PyMol is a visualization program, so it is not really meant for manipulating PDB files in a way you describe.

If you have coordinates of two independent molecules - a receptor (presumably a protein) and a ligand - there is no simple way to put them together. Your choices are: 1) dock the ligand, which is not trivial and most definitely can't be done in PyMol (unless there is some kind of a recent plugin for that purpose); 2) find a complex of a similar protein and a similar ligand and try superimposing your structures onto that complex. Option #2 is mostly a quick fix for visualization purposes, as you would still have to dock the ligand properly or at least minimize the complex.

ADD COMMENT

Login before adding your answer.

Traffic: 1495 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6