VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Thu Oct 14 2004 - 09:54:45 CDT

Hi,

On Wed, 13 Oct 2004 16:05:01 -0700 (PDT), Shirley Li <li19104_at_yahoo.com> 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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-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"