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