Jmol developers and users: At http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm, about two-thirds of the way down, you will see a new idea in solvent/molecular surfaces. Selecting only a subset of the atoms displays only the corresponding subset of the overall surface -- a surface "fragment". Drawing surface fragments is possible now because we are using isosurfaces, and we have the option to indicate "no value" for a surface-defining point.
The idea comes from a conversation I had recently with Chris Larsen of Vecna Technologies. He was interested in proper depiction of selected binding sites in enzyme models. For these depictions one wants just the part of the overall molecular surface that corresponds to the binding site. And it could be useful to color different fragments different colors. This is a proposed change to the "old" way where selecting a subset of the atoms draws a closed surface around them, regardless of whether that surface goes right through other nonselected atoms or not. My feeling is that that "feature" was really a bug, but if others feel otherwise, I can add it back in as a (nondefault?) option. Q: Do you like this idea? Q: Does anyone want to retain the "old" way? Q: Should I allow for the option? Q: If so, which should be the default -- subselection gives fragment or subselection gives closed surface? Bob ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
