VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Sat Apr 30 2011 - 04:34:27 CDT

On 2011-04-30 01:43:55AM -0500, Moutusi Manna wrote:
>
>
> Dear all,
>
> As we all know, in vmd, we can rotate or translate molecule using “VMD MAIN – Mouse –Rotate Mode/ Translate Mode”.
>
> But can I measure the extent of rotation (in degree) or translation (in Å)?

I'd like to know if this can be done graphically as well. I've just generally
just calculated the appropriate transformatoin matrix for precision operations
like that. (See node190 below)

To use manual translation:
You start with using atomselect to select the set then you can use the
commands instantiated by the selection:

#select all atoms in in top molecule loaded
set allatom [ atomeselect top "all" ]
set tmatrix { 1 0 0 0 } { 0 0 -1 0 } { 0 1 0 0 } { 0 0 0 1 }
#rotate about global x axis +90 deg (1pi rad)
$allatom move $tmatrix

>
> After modifying its location, is it possible to save molecule in pdb format?
>

set allatom [ atomselect top "all" ]
$allatom writepdb filename-translated.pdb

see:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html#ug:ui:text:atomselect
http://www.ks.uiuc.edu/Research/vmd/current/ug/node190.html
http://www.ks.uiuc.edu/Research/vmd/current/ug/node195.html 

-- 
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Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl_at_uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
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