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
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.
Albion E. Baucom
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