Warren,
I am able to create symmetry-related molecules by typing the symexp
command into the PyMol window interactively, but including the
identical command in my script (see below) does not work. This is
frustrating, as I need to create H-bonds to the symmetry molecules,
and now must type a
Kelley,
Unfortunately PyMOL doesn't have object-specific Z-clip. (That is a
cool idea though, perhaps in the future...)
The closest thing to this you can accomplish is to selectively show or
hide the surface on certain atoms in order to create a view which shows the
full ligan
As some of you may already know, we now have a freelance writer working with
us to rewrite/improve the PyMOL manual. This has been made possible through
the contributions of PyMOL licensees (specifically: Shering-Plough, Incyte,
Pfizer, Karo-Bio, as well as many other small contributors -- t
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 resoundin
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 acc
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
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
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 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 object
