Jmol Developers, I have just checked in some nice functionality for "connect" in 11.1. This is an old problem that was probably resolved, but I still ran into it on a recent project and decided there could be a simple solution.
Problem: You use "connect" to make new bonds, but then after that you want to target just those bonds and give them certain characteristics of radius and color/translucency. (Sounds familiar, right?) Solution: Two new capabilities of connect: connect ... [color/translucency] connect ... radius x.x for example: connect (_C) (_N) translucent red # make all (existing) the carbon-nitrogen connections translucent red connect 1.0 2.0 (_C) (_N) translucent red create # make new carbon-nitrogen connections translucent red connect (ligand) (protein) radius 0.1 yellow # make all (existing) ligand-protein connections yellow, with radius 0.1 The command can be as simple as: select * connect yellow Using connect in this simple way is much like set bondmode AND color bonds ... wireframe ... but it's more powerful, because the bonds don't have to be there already, and we can select bonds based on length as well as atoms. And, in addition, with "connect" one can select two different sets of atoms, one for one end of each bond and one for the other: connect (_C) (_N) radius 0.2 This is simply not possible using wireframe, where only a single set of atoms is defined. 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-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
