> > Hello all. > I am relatively new to pymol, so please excuse me if > these questions > are too simple for the list as a whole. I am running 0.90 on a Linux > system by way of introduction. > > 1) What is the easiest way to select one molecule out of > several on the > screen and translate it independently from everything else? I try > selecting it. but moving the mouse while holding the mov button still > translates everything.
Select "3 Button Editing Mode" from the mouse menu (or click on the mouse matrix, or simply type "edit_mode"). Ctrl-middle click on one atom in the molecule you wish to translate. A white ball should appear on that atom. Then shift-middle-click on that same atom to translate the molecule, or shift-left-click to rotate it. (If you click on other atoms in the molecule, only that fragment, relative to the ball will be translated) When done, click the Unpick button, or type "unpick", or ctrl-middle click away from any atoms to clear the picked selection. > 2) Is there an easy way to superimpose many molecules > independently? I > know that I can do individual pairwise alignments, but that > seems like a > good way to let more errors creep into the process. Not really. "fit" and "align" give you pairwise alignments -- there isn't any multiple-sequence-alignment capability in PyMOL yet. > 3) Is there an automated way to take HET groups in a > structure read from a > PDB file and make independent molecules out of them? The following commands will move the heteroatoms into a separate object: create hetobj, hetatm remove hetatm and not hetobj Cheers, Warren
