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
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