Raj, There are many programs that will give you an RMSD per residue difference between your bound and un-bound protein. Some will even write the RMSDs to the B-factor column of your PDB. You can then visualize regions in your protein that have structural changes/movement in the bound vs. unbound by using B-factor putty in Pymol or coloring by B-factor.
I refer you to a previous post on the subject in the CCP4BB archives: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14496.html On Mon, Nov 15, 2010 at 1:07 PM, Goragot Wisedchaisri < gora...@u.washington.edu> wrote: > I would first calculate least square superposition of the first monomer > between 2 structures (one to be fixed and one to be moved) using a program > such as lsqkap or any other programs suggested by others. You may need to > define a relevant region for the superimposition. > > Then take the output of the moved structure and calculate another least > square superposition of the second monomer in the dimer to the second > monemer of the fixed structure. Look at the rotation and translation matrix > from the output (or log file). That will give you information of how the > second monomer is different in the 2 structures. You can calculate the > orientation difference (in degrees) from trace of the rotation matrix. > > Alternatively, after the first monomers are superimposed, you can use > program lsqman (or other programs that calculate rmsd of the second monomers > without doing least square superposition) if you prefer an rmsd value > instead of a rotational angle. > > George Wisedchasri > > On Sun, 14 Nov 2010, E rajakumar wrote: > > Dear All >> I have two structures of homo-dimeric protein complex with different DNA. >> I want to calculate RMS deviation between second monomer from these two >> complexes by fixing superposed first monomer. >> >> This I require to know what is the effect of DNA on relative orientation >> of two monomers in the dimer. >> >> Previously I was using MOLEMAN2 to do this calculation. >> >> Please can you suggest me any other program to do this calculation. >> >> Thanking you >> Raj >> >> >> E. Rajakumara >> Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering >> Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 >> (Mobile) >> >> -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Lab: 1-301-594-9229 E-mail: fairman....@gmail.com james.fair...@nih.gov
