[Molvis-list] Advice on rendering superposed pdb files

[abi_chem at iiit.net]

Dear Prof. Bernstein,
We have developed a simple algorithm for superposing pdb files for two
base pairs and creating the pdb file for the superposed pairs. In the
superposed pdb file we have provided the two base pairs respectively with
different temperature factors and different chain ids so that they may be
viewed in different colors. Unfortunately, the rendering in Rasmol is not
coming out at all well. The two gif files show the quality of rendering in
different modes and the .pdb file is the file corresponding to the first
superposition step.
Could you please suggest a method for a better rendering using Rasmol or
any other software?
Thanking you in advance.
Abhijit

Dr. Abhijit Mitra
Professor
IIIT Hyderabad
Hyderabad 500032
India