Hi Hernando, “Best” depends on personal preferences, but there are two main approaches. (1) draw pseudobonds between the two structures. This could be done by listing specifications of the pairs of atoms in a text file (pseudobond file) and reading it in with Pseudobond Reader, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html> ...or by writing a command script with distance measurements between all the pairs of atoms. You could hide the distance labels afterward, for example with the Distances tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances> You can control pseudobond line style, line width, color, or change them to sticks in the Selection Inspector or with the “setattr” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> (2) create a simple text file in BILD format describing cylinders or 3D arrows between the pairs of points. Then opening the file (name ending in .bld) shows the objects. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 11, 2019, at 8:42 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear UCSF-Chimera, What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this? Thanks Hernando