[Chimera-users] Problem with RMSD calculation

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 5 14:36:47 PST 2012

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 Pettersen
                        UCSF Computer Graphics Lab

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