Hello: Not exactly sure what you are asking here but if you want to calculate the distance moved you could use the distance command: distance atomx, atomy to tell you how far atoms in the residues has moved.
you can also calculate dihedrals (ie/ X values) using the dihedral command dihedral name_you_give, atomw, atomx, atomy, atomz so you could compare the dihedral values for rotation of the residue. but you are more likely to want rotation around axes or relative movements, in which case using the actual coordinates of the atoms and doing the math (ie. movements of centriods of the residues around a central axis) is going to yield more meaningful results. You can even get the coords of an atom in pymol without looking at the pdb by turning on the label wizard and selecting an atom. Cheers, JTM "We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated." Linus Pauling, Nobel Laureate 1954 "...everything that living things do can be understood in terms of the jigglings and wigglings of atoms." Richard Feynman, Nobel Laureate 1965 **************************************** Jason Thomas Maynes, MD/PhD Department of Biochemistry and Molecular Biophysics Resident in Anaesthesia and Paediatrics Faculty of Medicine Washington University in St. Louis jmay...@biochem.wustl.edu **************************************** > Hi, > > I am a new user of Pymol. I am currently working on mutant protein > structures and I would like to compare the side chain shift between the > mutant and wild-type structures. May I know how could I measure the side > chain shift? > > Thanks a lot! > > > Phoebe > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642_______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
