VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sun Jul 27 2008 - 02:16:58 CDT

an addition to what I wrote before:
did you try to make two selections containing the only the atoms
you mentioned and to determine the transformation matrix by "measure
fit"?
(check manual p166f for usage)
I do not know, though, if it works, for only two atoms in each of
the selections, but you could try.

eddi

On Jul 27, 2008, at 1:52 AM, Schreiner Eduard wrote:

> Hi Roman,
>
> maybe you would like to take a look at the
>
> move [trans bond ....]
>
>
> command (just search for "move [ trans bond" in the manual. In the
> current from the vmd web page it is on pp 160f).
> instead of "bond", you also can specify an axis like
>
> $sel move [trans bond {0.0 1.0 0.0} {0.0 0.0 0.0} 90 deg]
>
> Using something similart, you should be able to rotate your system
> in the appropriate way.
> Since you have already positioned one of the atoms at the correct
> position, you will have to determine the angle for the rotation and
> the axis of rotation. However, may get quite tricky. Maybe there is
> a simpler solution.
>
>
> eddi
>
> On Jul 26, 2008, at 11:31 PM, Roman Petrenko wrote:
>
>> I have two identical molecules (described by the same psf file), but
>> with different coordinates. Each molecule has some inner bond CA-CB,
>> the question is how to align molecule2 with molecule1, so that the
>> specified bond in both molecules have EXACTLY the same coordinates.
>>
>> I tried fit - method and it didn't work.
>>
>> So far i've managed only to bring two CA atoms from each molecule to
>> the same spot.
>>
>> Thanks.
>>
>> --
>> Roman Petrenko.
>> Physics Department
>> University of Cincinnati