[Chimera-users] RMSD between ensemble of a protein and its paralogue crystal structure

[Thomas Evangelidis]

Dear UCSF Chimera developers,

I want to calculate the RMSD between a MD trajectory of a protein and the
crystal structure of its paralogue protein. I have looked though the
Ensemble Match and RMSD Analysis pages but these applications work for the
same proteins (correct me if I am wrong). Is there any way to provide an
alignment file to Chimera and calculate the time series of the RMSD between
the two paralogues?

Thanks in advance,
Thomas



-- 

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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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