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 GangopadhyayJunior Research FellowDBT Centre for BioinformaticsPresidency UniversityKolkata, India
Eric Pettersen
UCSF Computer Graphics Lab