[Chimera-users] Estimated RMSD after using Modeller feature

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 21 10:50:16 PDT 2012

Hi Claudia,
The "estimated RMSD" is a model quality score calculated by the Sali lab's Model Evaluation Server. For descriptions of scores, literature references, and links to more information at the Sali lab website, click the Help button on the Model List dialog in Chimera or see here:

"Estimated RMSD - TSVMod predicted Cα root-mean-square deviation (RMSD) of the model from the native structure (see Eramian et al., Protein Sci 17:1881 (2008))"

So if you follow the link to the Eramian paper (from the URL above) it should explain more about the calculation.  I don't know the exact answer to your question, but I imagine there may be additional restraints from the extra N-terminal residues.  Also, the model-building involves some randomization, so even multiple models from the same template would have different scores, including different estimated RMSD values.  Finally, this estimated RMSD is not relative to the template, but relative to the (unknown) "real" structure of the protein you are trying to model.  That is why it is "estimated" rather than an exact calculation.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 21, 2012, at 7:26 AM, Claudia Fernandes wrote:

> I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function.
> I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)?
> As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it.
> Any help would be welcome.
> Regards,
> Cláudia Fernandes

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