Wonderful, Bob! > 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.
I agree. This is how surfaces work (or at least can work, don't remember now) in Chime and, among other things, opens the way for a very interesting feature that Eric Martz designed into Protein Explorer: the "contact surfaces", where a fragment of surface is generated on either the ligand or the receptor, and the surface is colored according to distance to the other moiety. For that, the ability to color the surface in a stepwise gradient is needed (say, select 5 A distance and color grey, then 3 A distance and color magenta, then 2 A distance and color pink). Next week I may have time to specify this in more detail (or Eric will do). > Q: Do you like this idea? Definitely > Q: Does anyone want to retain the "old" way? Don't think so. They look nice, but they are false: the molecule continues, but the surface closes. > Q: Should I allow for the option? > > Q: If so, which should be the default -- subselection gives fragment or > subselection gives closed surface? Fragment. ------------------------------------------------------------------------- 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
