VMD-L Mailing List

From: Shirley Li (li19104_at_yahoo.com)
Date: Fri Oct 15 2004 - 09:33:00 CDT

Hi Justin,
 
Many thanks for all those information, I do appreciate greatly! They are really helpful for me.

Regards,

Shirley

Justin Gullingsrud <justinrocks_at_gmail.com> wrote:
Hi,

On Wed, 13 Oct 2004 16:05:01 -0700 (PDT), Shirley Li
wrote:
>
> Dear VMD users,
>
> I have two questions regarding VMD:
>
> 1) With VMD, how to align a PORTION of two or more structures, say the
> region from residue 35 to residue 50, instead of the whole structures, and
> then get the corresponding RMSD value?

# Assume the reference molecule has id 0, and the one you want to
align has id 1 (the id's
# appear next to the names of the molecules).
#
# Create a reference structure
set ref [atomselect 0 "resid 35 to 50"]

# Create a selection to align
set sel [atomselect 1 "resid 35 to 50"]

# Move molecule 1 onto molecule 0
set all [atomselect 1 all]
$all move [measure fit $sel $ref]

# Compute the rms distance:
set rms [measure rmsd $sel $ref]

# Or use mass-weighted RMSD fitting:
$all move [measure fit $sel $ref weight mass]
set massrms [measure rmsd $sel $ref]

>
> 2) What's the algorithm for VMD to assign the secondary structure for each
> residue of a protein?

VMD uses the program Stride to compute secondary structure.
Apparently there is a recent article describing it:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=441567

Cheers,
Justin

>
> Any help/information will be highly appreciated.
>
> Shirley
>
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