pymol-users-boun...@lists.sourceforge.net wrote on 09/20/2006 07:28:00 AM:
> Paul, > > I think the reason the surface coloring "spills over" is because > there are some surface triangles that are shared by the selection you > want (red) and the neighboring residues (grey)... So it should work > if you only use one selection, by saying something like: > load my_protein.pdb, > show surface, > color grey, > color red, (something at the center of the pocket) expand 8 > > Hope this helps, > > -bob > I think this is the right approach. If you invert the selection for the other surface, you should be able to avoid having triangles in both surfaces. Like this: load my_protein.pdb create pocket, chain a create rest_of_protein, chain a color red, pocket color gray, rest_of_protein show surface, pocket and resi 10-15 show surface, rest_of_protein and not(resi 10-15) set transparency=0.5, rest_of_protein This gave a sharp edge when I just tried it. If you don't like the jagged look of the edge, try changing the color statements above, to color gray, pocket color red, pocket and resi 10-15 color gray, rest_of_protein Now your red triangles will fade into the semi-transparent gray surface. Hope that helps, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
