VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 19 2012 - 07:28:09 CDT

On Thu, Jul 19, 2012 at 2:17 PM, Víctor <victor.gil.sepulveda_at_gmail.com> wrote:
> I mean the superposition algorithm for rmsd calculation. In a script the
> command would be measure fit if i'm not wrong.

ok. from the sources:

// find the best fit alignment to take the first structure into the second
// Put the result in the matrix 'mat'
// This algorithm comes from Kabsch, Acta Cryst. (1978) A34, 827-828.

please note, that for up to three atoms in the selection,
different approaches are used.

HTH,
    axel.

>
> On Thu, Jul 19, 2012 at 1:55 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Thu, Jul 19, 2012 at 12:06 PM, Víctor <victor.gil.sepulveda_at_gmail.com>
>> wrote:
>> > Dear All,
>> >
>> > I've been playing around with a C++ implementation of a superposition
>> > algorithm. When I've compared the results with VMD, I've noticed that
>> > those
>> > are different, but equal to other implementations of the same algorithm
>> > I'm
>> > using, so my code is correct.
>> >
>> > Does anybody know which superposition algorithm is VMD using?
>>
>> can you be a bit more specific about what "superposition"
>> you are talking about. i.e. which commands exactly you
>> are running in VMD.
>>
>> thanks,
>> axel.
>>
>> >
>> > Thanks!
>> >
>> > --
>> >
>> > Víctor Gil Sepúlveda
>> > E. Informatica - FIB - UPC
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
>
> Víctor Gil Sepúlveda
> E. Informatica - FIB - UPC 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.