This question just came in about the sequence viewer...I'm anonymously copying it to the mailing list since it is bound to come up frequently:
> Hey Warren, > > I just downloaded the new version of PyMOL and was playing > with the new sequence view. Is it possible to do a > structural alignment (with 2 or more structures) and then > view this alignment in sequence view? Can you load/input > your own sequence alignments? PyMOL's sequence viewer does not currently have any alignment display capabilities, but that functionality is definitely planned for the 0.97 or 0.98 releases. In the meantime, the best use of the sequence viewer is probably as a shortcut way to locate or alter the way specific regions of a molecule are displayed. However, you can perfom manual alignments with the sequence viewer by using selections of equal length on two separate molecules. For example, if you select "sel02" including a set of N residues in "il2" and N residues in "1tii", the following command will superimpose the two structures using that selection pair_fit il2////ca & sel02, 1tii////ca & sel02 Also note the following *tentative* sequence viewer controls: Left button Create/edits selections by dragging w/ Shift - extend selections w/ Control - centers about current selection Middle button Center residue w/ Control - Zoom residue w/ Shift - Center region w/ Control + Shift - Zoom region Pop-up Menu: on Selection: apply action to complete selection off Selection: applies action to just that residue. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
