Re: [PyMOL] make cartoon from carbon atom trace?

[Lieven B. <li...@ul...>]

On Monday 05 January 2004 23:18, Ann Mullin wrote:
> I have some PDF files which only contain the backbone carbon atoms,
> and I would like to  use PyMOL to show a cartoon representation of the
> backbone.  Any suggestions?

There is a setting called "cartoon_trace". By default it is set to zero and 
PyMOL will not connect Calpha atoms when the other atoms are absent. You can 
change the setting in the corresponding menu, or with the command

set cartoon_trace,1

PyMOL should now draw cartoons through the Calpha positions, although it might 
get confused if there are multiple chains in the PDB file and connect the 
last atom of one chain to the first of antoher. In that case it will be 
necessary to create separate objects for the different chains.

There is an analogous setting "ribbon_trace" for the ribbon representation. In 
this case, separate chains do not appear to get connected.


Best wishes to all for 2004,

-- 
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel