Sreetama, See the following URL whether it is useful to solve your issue
http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar > Dear all, > When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > should be reported - an overall value which may be inflated due to the > deviations in the loops, or separate values for the core and loop regions? > What is the best way to calculate the RMSD for superposition of the cores > - should I prepare a separate PDB file by removing the coordinates of the > loop residues and then superpose? > > Thanks in advance, > Sreetama das, > PhD student, > Physics, IISc > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > Could you kindly confirm the safe receipt of the mail please. All best wishes and regards, Yours sincerely, Dr. K. Sekar, Ph.D. Associate Professor Supercomputer Education and Research Centre Room No. 341, old Ecological Sciences Building (Second Floor) Indian Institute of Science Bangalore 560 012 INDIA E-mail: se...@physics.iisc.ernet.in se...@serc.iisc.ernet.in Tel: 91-(0)80-22933059/22933060/23600551 Fax: 91-(0)80-23600085 Home page: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html Google Scholar: http://scholar.google.co.in/citations?hl=en&user=CT0Z5kIAAAAJ -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
