Re: [PyMOL] Super and Align missing residues

For anyone who has found this thread, I've taken some time and put together an alignment + RMSD script for Pymol (using BioPython). You can find it on GitHub, here . It's a bit overkill, and only handles single chain proteins, but

Re: [PyMOL] Super and Align missing residues

Hi Nathan, Thank you very much for the files and instructions. I can reproduce the problem. I haven't seen this before and don't know yet what's going wrong, we will investigate. Cheers, Thomas > On Jun 28, 2018, at 10:50 AM, nclem...@cs.utexas.edu wrote: > > The alignment in this example

Re: [PyMOL] Super and Align missing residues

Hi Nathan, Sounds like you are doing everything correct. Would it be possible to send me the input files? Thanks, Thomas > On Jun 26, 2018, at 10:58 AM, Nathan Clement wrote: > > Hi, > > I'm trying to compute the interface RMSD (iRMSD) between two protein pairs > that are highly similar

[PyMOL] Super and Align missing residues

Hi, I'm trying to compute the interface RMSD (iRMSD) between two protein pairs that are highly similar (might have a few missing residues, but are otherwise identical). Right now, my code does something like the following for protein pairs "gold" and "test" (receptor has chains A+B and ligand has