Hi Amitoj,

If R can run external system commands then this is possible.  Use bio3d to write a PDB file and then use R to start Chimera from the command line with the PDB file name as an argument, as documented here:

If you don't know how to run external commands from R, you would probably have to ask about that on the R mailing list.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu