VMD-L Mailing List

From: Marzieh Dehghan (m_dehghan_at_ibb.ut.ac.ir)
Date: Sun Jul 20 2014 - 15:31:26 CDT

Dear every body

I have two pdb files which are resulted from docking. I want to merge them
and evaluate their conformational changes. after uploading two pdb files
into vmd, I have two questions?

if I want to use tcl, please let me know the following common line is
correct?

set sel [atomselect top "name CA"]
set sel1 [atomselect 1 "name CA"]
set fitmat [measure fit $sel $sel1]
$sel move $fitmat

2- I use extensions-modelling-merge structure of vmd, but I confronted an
error. I would like to know should I upload pdb and psf file (both of them)
in the merge structures window?

thanks in advances

best wishes

marzieh