[Chimera-users] Problem with RMSD calculation

[Aditi Gangopadhyay]

Dear Sir,
I have been using the 'rmsd' command for calculating RMSD. Yes, this solves
my problem! Thank you so very much!

Regards,
Aditi.
On Tue, Nov 6, 2012 at 4:06 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

>   On Nov 2, 2012, at 1:33 AM, Aditi Gangopadhyay wrote:
>
>  Dear Sir/Madam,
>
> I've been using Chimera for the calculation of RMSD of two ligands
> associated with a protein. (In my specific case, it is the same ligand, one
> being associated with the usual protein, and the other with the protein
> bound to a small molecule). However, I have had a problem with this, since
> the RMSD values are differing when I select my concerned ligand using GUI
> and when I select using the ctrl+drag way. I would be very grateful if you
> would kindly tell me where I'm going wrong in my selection or somewhere
> else.  Thank you so much in advance for your help!
>
> Regards,
> Aditi.
> --
> Aditi Gangopadhyay
>
> Junior Research Fellow
> DBT Centre for Bioinformatics
> Presidency University
> Kolkata, India
>
>
> Hi Adit,
> I'm assuming you are using the "match" or "rmsd" command to measure the
> RMSD.  The problem with using a selection as an argument to the command is
> that the atoms are matched in the same order as they were selected.  This
> is fine if you selected the atoms one by one (with shift-control-click),
> but a control-drag adds the atoms to the selection in an arbitrary order.
>  Probably the easiest way to specify your ligand in the match command,
> assuming there is only one instance of the ligand in each model and the
> models are #0 and #1 (and the ligand name is, say, "XYZ"):
>
> rmsd #0:xyz #1:xyz
>
> --Eric
>
>                          Eric Pettersen
>
>                         UCSF Computer Graphics Lab
>
>                         http://www.cgl.ucsf.edu
>
>
>


-- 
Aditi Gangopadhyay

Junior Research Fellow
DBT Centre for Bioinformatics
Presidency University
Kolkata, India
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