> 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
set ribbon_color, green Same goes for cartoon_color, sphere_color, surface_color, dot_color, and mesh_color. Note that these are for global, full-object, or full-state uniform color. If you need finer-grained color control, then you have to create separate objects as Garrett suggested. > 3) Is there a way to change the particular rendering of the > beta-strands at a paritcular residue. If you use 'flat Yes -- new in version 0.95: flag no_smooth, selection, set rebuild For example, if residue 200 is shown both in sticks and in a flat sheet, you can force that sheet to pass through the resi 200 CA position as follows: show sticks, resi 200 and (pro/n | !*/n+c+o+h) show cartoon flag no_smooth, resi 200, set rebuild The alternative, which I personally find distasteful, is to drag the CA atom position into the plane of the sheet using the mouse in editing mode (ctrl-shift-left-click-and-drag) in order to create an unreasonably long CA-CA bond. This is best done with a separate copy of the object so that the cartoon itself doesn't move. > 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? PyMOL can't do this -- you'd need to export to POV-Ray...but PyMOL's current export code is quite dated. Cheers, Warren
