Bugs item #972612, was opened at 2004-06-14 17:41 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=972612&group_id=23629
Category: None Group: None >Status: Closed >Resolution: Duplicate Priority: 5 Submitted By: jimM (meekjl) Assigned to: Miguel (migueljmol) Summary: "set solvent" vs select Initial Comment: I like to be able to look at the surface of a protein in the vicinity of a ligand. (Or the surface of a ligand and an associated protein in wireframe). In chime/rasmol, I can create a surface after selecting the ligand or protein, and see the surface for that whole selection. In Jmol, only the surface of a ligand where the atoms are distant from the protein generate surfaces. Is there anyway to defeat this characteristic? ---------------------------------------------------------------------- >Comment By: Miguel (migueljmol) Date: 2004-07-07 10:29 Message: Logged In: YES user_id=1050060 changed to bug [986431] ---------------------------------------------------------------------- Comment By: jimM (meekjl) Date: 2004-06-14 21:03 Message: Logged In: YES user_id=1061788 I was wrong -- one can selectively see the surface of a ligand/protein interaction in chime, but not rasmol. To see the chime version, I went to the online demo: http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.ht m and selected heme + protein select protein; surface molsurface ; select not protein; spacefill off; wireframe clearly shows the cavity with no surface on the ligand. "select not protein; surface molsurface" does the converse. In contrast, in rasmol, select protein solvent on dots on only generates a surface on the entire molecule, not only the residues selected. I believe the chime version is more useful. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-06-14 18:55 Message: Logged In: YES user_id=1050060 Jim, Thanks for submitting this. I am going to need your help in understanding the problem. I do not have access to chime, but can use RasMol 2.6b2. When you say 'surface' I assume that you are referring to the dots representation of the VDW or solvent accessible surface. Please confirm. I wrote this code a long time ago and have not looked at it recently. At the time I did not understand RasMol very well. Are you saying that in RasMol only calculates the surface for the atoms that are selected? That is to say ... is the surface calculated as though only the selected atoms were present in the file? Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=972612&group_id=23629 ------------------------------------------------------- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
