VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon Jul 23 2001 - 12:34:16 CDT

On Mon, Jul 23, 2001 at 02:01:43PM +0200, Alexey Kozlenkov wrote:
> Hi, I have three simple questions:
>
> 1) is it possible in VMD to merge two PDB files into one, or to do the same with selections from two different pdb structures opened in vmd.
>

No, but you can do this using the psfgen tool available from NAMD,
www.ks.uiuc.edu/Research/namd/.

>
> 2) how can I re-center the view on the visible part of the molecule, (say, I made the heme the only thing visible in a hemoglobin structure, and now want it to rotate around its mass center)

Change your mouse mode to "center", either through the Mouse menu or (more
easily) by pressing 'c' on the keyboard. If you then click on an atom,
release, then rotate the scene with the mouse as before, the scene will rotate
about the selected atom.
 
>
> 3) is there an easy way (a command or a script) to superpose two related protein structures, and then to color them according to which areas differ most?

'easy' sort of depends on how familiar you are with VMD/Tcl scripting. You
can superimpose related structures by creating two atoms selections, one from
each molecule, and each containing equal numbers of atoms, then using the
'measure' commands to fit them. Something like the following should work:

        set sel0 [atomselect 0 "backbone and resid 10 to 50"]
        set sel1 [atomselect 1 "backbone and resid 15 to 55"]
        $sel0 move [measure fit $sel0 $sel1]

This selects equal numbers of backbone atoms from each molecule, then moves
the first molecule on top of the second. Note that you can augment the
"measure fit" command with a weight to do a weighted RMSD, e.g.:

        measure fit $sel0 $sel1 weight mass

As for coloring by distance, that's a little trickier, but reasonably
straightforward. The general strategy would be to find the distance between
each corresponding atom (or perhaps each residue? it's up to you), assign
that value to either the occupancy (or beta) value for each atom, then color
by occupancy (or beta). We often use occupancy and beta as 'user' fields
which can be assigned arbitrary values.

Justin

>
> Thanks,
>
> Alex 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D