Dear PyMol users,
I realize the following may be somewhat basic questions, but after
fiddling with the program a while and trying out example scripts from the
web, I cannot seem to get things to work properly. The last question is
kind of advanced and would have cool effects if someone knows how to get it
working (I'm also using MacPyMol 0.95).
1) I would like to show certain residues and have no problem getting the
ones I want selected and displayed as sticks or whatever. The problem is
color. When I change the color of the selection, it changes the color of
the associated section of the ribbon. I would like to leave the ribbon, say
green, and show the residues in yellow. Is there a way to uncouple the
color assignment of the ribbon and the residue. For example, if I load a
molecule, make the cartoon diagram, and color it green it's fine. If I then
select, say, all the cysteine using:
Select allcys, (resn cys)
Show sticks, allcys
Color yellow , allcys
The sticks turn yellow, but so do the small sections of the ribbon. How do
I keep the ribbon green?
2) When selecting specific sidechains, it is often preferable to choose
only the sidechain atoms instead of the sidechain+backbone. In the good ol'
molscript days you would say select and not c or n or o but if you do that
in pymol it thinks you mean all carbon, nitrogen, and oxygen atoms instead
of their id in the PDB file. I'm sure this is worked out but I don't see it
in the example scripts I've found on line.
3) Is there a way to change the particular rendering of the beta-strands at
a paritcular residue. If you use 'flat sheets,' which one often does, then
the path of the sheet doesn't always intersect the the alpha-carbon of the
residue and you wind up with 'floating' sidechains.' This is generally ok,
but for some altering the path to the type of rendering where the strand
passes through the CA would be fine and wouldn't look weird. Is there a way
to set this kind of rendering for particular residues?
4) This is the hard but cool one. Is there a way to make a particular atom
or object the light source for an image. You can imagine if you turned off
all other lighting and put your omnidirectional light on your cooridnated
metal atom it could look pretty cool (or just have a dim headlight seeting).
Does anyone know how to arbitrarily set the lighting in this fashion?
Thank you all so much.
Tony
