VMD-L Mailing List

From: Jim Pfaendtner (jpfaendt_at_hec.utah.edu)
Date: Mon Aug 27 2007 - 10:58:31 CDT

Leonardo,

Thanks for the help and pointing me to that post. I tried exactly
what you suggested in the previous post but I am getting a strange
error. Here is my VMD output. I tried setting the "order" list both
from $sel2 and $sel1 and I also did the fit before re-ordering just
to make sure that worked too.

Thank you!
Jim

% set sel1 [atomselect 0 "index 1 2 3 4"]
atomselect0
% set sel2 [atomselect 0 "index 5 6 7 8"]
atomselect1
% measure fit $sel1 $sel2
{-0.707626342773 -0.53004014492 -0.467249810696 -117.393280029}
{0.621917784214 -0.78109151125 -0.0558064132929 56.5098266602}
{-0.335385233164 -0.330081045628 0.882362306118 -19.8030891418} {0.0
0.0 0.0 1.0}
% measure fit $sel1 $sel2 order {8 7 6 5}
measure fit: order parameter contains out-of-range atom index
% measure fit $sel1 $sel2 order {4 3 2 1}
measure fit: order parameter contains out-of-range atom index

On Aug 25, 2007, at 12:31 AM, Leonardo Trabuco wrote:

> Dear Jim,
>
> On Fri, Aug 24, 2007 at 04:58:51PM -0600, Jim Pfaendtner wrote:
>> I am selecting 3 alpha carbons from one molecule and 3 alpha carbons
>> from another molecule and I would like to align the two molecules
>> based on the selection of these 6 atoms.
>
> It is not uncommon that the alignment algorithm doesn't work well with
> such a small number of atoms. You may want to try using 4 atoms
> instead
> (you could create a dummy atom and set it to the geometric center
> of the
> other 3 atoms); I believe that works better that using 3 atoms.
>
>> [...]
>
>> When I look at the resids in each of my selections, the selection is
>> ordered from highest resid to lowest. I guess this has something to
>> do with the way the atoms are searched in the pdb during atomselect,
>> i.e., the order that I specify (selection 1), (selection 2),
>> (selection 3) does not matter...
>
> That's correct, it does not matter: the selection is ordered by
> increasing index values, if you wish. This is an efficient and general
> behavior. If the order mattered, what would be the order of the
> following atom selection? :-)
>
> atomselect top {index 10 or index 5 or index 10}
>
>> I think frequently the alignment procedure is used on two identical
>> proteins, so this is probably not an issue because the residue
>> numbers are all the same.
>>
>> One idea I had was to perform all six atom selections separately and
>> then form a concatenated atom selection in the order I want. Is this
>> possible?
>
> Nope.
>
>> Does anyone else have a suggestion how to do this alignment?
>
> Check out this message from a couple of days ago:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10172.html
>
> I short, you can give an order parameter to 'measure fit'.
>
> Cheers,
> Leo
>
> --
> Leonardo Trabuco, Ph.D. student
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign