Dear Ashish,

To my knowledge GDT-score compares only C-alpha positions (Zemla et al, PMID: 10526349) and I have the notion that the same applies to TM-score, although not explicitly stated in the original publication ( http://zhanglab.ccmb.med.umich.edu/TM-score/faq.html - read the 2nd answer). There is another metric used in CASP8 called GDT-sc ( http://kinemage.biochem.duke.edu/suppinfo/CASP8/methods.html#gdcsc) which quantifies the differences in side-chain conformations.

I don't know if you measured the whole-atom RMSD or just C-alpha RMSD, but practically you won't observe any differences in side-chain conformations with SCWRL4 if your sequence identity is high.

HTH, Thomas

On 7 April 2011 02:18, Ashish Runthala ashishr@bits-pilani.ac.in wrote:

> MODELLER9v9 models couldn't be improved further with SCWRL4. There was no > difference in the GDT, TM_Score and RMSD statistics of model with and > without SCWRL usage. > So are all the side chain rotamer loci best optimized with the Calpha atom > topologies? > > Thanks > Ashish > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >