Re: [Chimera-users] Problem with RMSD calculation

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

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@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
-- Aditi Gangopadhyay Junior Research Fellow DBT Centre for Bioinformatics Presidency University Kolkata, India

Dear all, in Ubuntu 12.04, 32 bit, I have the following error message when starting Chimera 1.6.2: "Error initializing OpenGL: X server is missing OpenGL GLX extension. Couldn't configure togl widget". Do you know a solution for this problem? Thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it
participants (3)
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Aditi Gangopadhyay
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Eric Pettersen
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sette@uniroma2.it