I am new to PyMol and spent the day getting use to the controls, learning the interface and reading the manual.
Now, I have a few questions. Before that though I want to let everyone know why I want to use PyMol I want to make high resolution, smooth (high frame rate) playing movies of the Ribosome. Ideally I would like to move seperate objects in the view separeately, that is have things "dock" in the movies. I dont know if PyMol will do this yet ... Now, the rRNA I have is phosphorus atom only, with some allatom proteins some CA-only proteins. PyMol opens the psueudo-atom rRNA as a cloud of atoms, presumably because it does not know how to bond these files. That is my first question. How, and what do I modify (bond definition file) to make it bond the adjacent atoms of the phosphorus only backbone? My second question for now is once I bond it, will Pymol be able to render a cartoon using the P atoms to interpolate? My only workaround ideas now are to take the pseudo-atom model, use CNS (generate.inp) to build in the rest of the bases, use that to generate the cartoon, and undisplay the stick representation (which of course will have completely bogus conformations). Im not sure what biases the built in bases will impose on the cartoon if PyMol uses them to interpolate the ribbon. At some point I would like to draw pseudo-bonds between base-paired pseudo-atoms, but I will see if I can do the above before that. Thanks! Albion Albion E. Baucom http://www.cse.ucsc.edu/~baucom
