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 it's

Re: [PyMOL] Super and Align missing residues

Hi Nathan, I have some insights for this issue. Basically the long gaps between the selected parts become too expensive in the alignment scoring. Changing e.g. the gap extension penalty leads to the expected result: # default is extend=-0.7, lowering to -0.6 super gold & contact_all, test, cycl

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 i

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 (