From: Marcos Sotomayor (
Date: Thu May 31 2007 - 01:29:50 CDT

Hi Alison,

You may also want to look at the Tcl scripts found at the end of the VMD
or at the end of the first unit in the NAMD tutorial:

By modifying your "frame0" and "sel" selections you will be able to
select any part of the protein to perform the corresponding alignments and
rmsd calculations. You will need to create a different selection
("selall") to move the whole protein during the alignment, besides the
parts that were used to perform the alignment. The "frame0" selection can
also contain parts of a protein in a different molecule (like the protein
crystallized in complex with another subunit loaded as a different
molecule) or the first repeat of your protein ("protein and backbone and
noh and resid 1 to 33"). Let us know if you need more help.


On Tue, 29 May 2007, Peter Freddolino wrote:

> Hi Alison,
> to start with, you may want to look at the RMSD Trajectory Tool plugin
> (,
> which lets you align frames and different structures based on certain
> selections and calculate the resulting RMSDs. This is usually a good
> step prior to other types of analysis as well. You can find it under the
> Extensions->Analysis menu of VMD.
> Best,
> Peter
> Alison Grinthal wrote:
>> I'm new to VMD and am wondering if someone can provide advice on the
>> best way to do the following:
>> I have a trajectory file from a pulling simulation, and I'm trying to
>> compare the structural details of the initial, early, and final
>> stages. So first I'm wondering how to overlay structures from
>> different frames, while specifying which segment to base the alignment
>> on. I'd also like to compare the structure of a given trajectory frame
>> with the published structure of the same protein crystallized in
>> complex with another subunit (which isn't present in the simulated
>> structure's psf file; it's a different pdb file).
>> More specifically, the protein is composed of sequential repeats, and
>> I'd like to analyze how the orientation between adjacent repeats
>> changes with pulling. To do this, I'd like to look at 2-repeat units
>> from different frames, but align them based only on the first repeat,
>> so I can see how the orientation of the second repeat changes relative
>> to the first.
>> Thanks very much for any advice.