VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Thu Nov 02 2023 - 12:58:25 CDT

Hi Vasista,
try this stride_by_pfrag.tcl script attached to this email.
Please bug me if this doesn't work for you. I'm also working on a
definitive solution for STRIDE.

Computing the Secondary Structure by fragment comes with a caveat. It may
result in less B-strands.
That is because the way they are defined depends on neighboring residues,
which may come from a different protein chain (fragment).

The scripts also solve a PDB format limitation due to fixed format. It
creates a tmp molecule for each fragment centers it prior to running STRIDE--0000000000000aa97d06092f2369--
--0000000000000aa98106092f236b--