Hi Kelley,
I just worked out a procedure to do this with VMD/Raster3D (oops, this is
the PyMol list ...). Anyhow, it boils down to that you can apply selective
bounding or clipping planes in Raster3D. In the case of a clipped surface
you want to use a bounding plane, which slices through an
Where can I find a list of what I can set with regard to ribbons and
cartoons. Currently the cartoons command just shows a thin round tube and
the ribbons command shows just a thin line.
I'd ideally like to have cartoonishly round ribbons with some of the
residues on them drawn in sticks. I'm a
Have you set your sheet and helix part in your pdb? For my personal case,
things you experienced happened when this part wasn't built.
I guess that PyMOL cannot find the secondary structures as softwares like
Rasmol can.
Try to determine your secondary structures with DSSP for example and to
paste
Hi Kristl
The problem is that the secondary structure of your protein hasn't been
defined in the PDB file. This is why the cartoon looks ike a tube. What
you need to do is type util.ss into the command line and this will
calculate some sort of secondary structure for you although it's not
that
Hello, while this is a simple question, I can't seem to find the answer
anywhere.
How do I select a specific hetatm:
The pdb file says:
HETBCL C 1 51
HETBCL C 2 66
HETBCL C 3 66
HETBCL C 4 66
HETBPH C 5 51
HET
Hi Carsten,
I appreciate your reply and I would assume that it makes impressive
graphics, but it sounds WAY beyond my meager abilities (I am struggling with
the Mac OS X version of Pymol after all and haven't ventured into the realm
of raster3D yet). I assume that since there has been a
