If you press 'Shift' key and move the mouse, then you can rorate it as well.

Try Chimera: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust

It can be done, it has been mentioned in the vmd list (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21427.html):

set sel [atomselect top "resid 10"] set com [measure center $sel weight mass] set matrix [transaxis z 45]

$sel moveby [vecscale -1.0 $com] $sel move $matrix $sel moveby $com

Here they rotate around Z axis.

I think, using TK console you will get only visualization of the rotated structure. If you want to rotate the residue and save the new coordinates, you have to rotate it using the 'Move' option. You can find it in the VMD Main window in 'Mouse' option.

Swapnil, but 'Mouse' option only allows to move the residue not rotate it.

If you press 'Shift' key and move the mouse, then you can rorate it as well.

Hi all, both options (TK and mouse options) can change and consequently save the coordinates. The mouse option is easier to use, since it has a graphic environment while the one from TK is way more accurate. So a "Recommend" to both answers is required.