I believe that you need to make these new objects to correct the problem, at least this is a quick fix that I have done in the past. There may be a more elegant solution:
load my.pdb, obj1 load my.pdb, obj2 [whatever to each obj] When loaded separately you don't have this problem. Cheers, JTM "We can be sure that if a detailed understanding of the molecular basis of chemo-therapeutic activity were to be obtained, the advance of medicine would be greatly accelerated." Linus Pauling, Nobel Laureate 1954 "...everything that living things do can be understood in terms of the jigglings and wigglings of atoms." Richard Feynman, Nobel Laureate 1965 **************************************** Jason Thomas Maynes, MD/PhD Department of Biochemistry and Molecular Biophysics Resident in Anaesthesia and Paediatrics Faculty of Medicine Washington University in St. Louis jmay...@biochem.wustl.edu **************************************** > 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 > > On 9/20/06, Paul Wilhelm Elsinghorst <p...@uni-bonn.de> wrote: >> Hi, >> >> >> please have a look at this image: http://pwe.no-ip.org/other/1.png >> >> >> I'm having trouble with the edge of a surface selection. It seems that >> there is always some more surface shown than the selected part. What I >> did is, that I selected the red part to show the surface in obj1 and to >> hide the surface in obj2 which is grey. obj1 and obj2 are copies of each >> other. I hoped that this would show a sharp border red/grey as I want to >> change the transparency in obj2 (grey) to fade out. >> >> >> How do I get pymol to show sharp borders and have no overlapping >> (dotted) parts as in the image? >> >> >> Paul >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share >> your >> opinions on IT & business topics through brief surveys -- and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
