I went and asked your question to Andrew Dalke, who is an expert in such things. Writing programs for visualising molecules is what he does for a living. The news is not good.
First of all, he says the "spt" format is a command format. See http://www.callutheran.edu/BioDev/omm/scripting_ch/molmast.htm for examples. select all; wireframe; dots off; wireframe off; backbone; wireframe 100; spacefill off; list molsurface transparent; select all; spacefill; set specular on; set specpower 20; define piece :A and 10, :A and 11, :A and 12; select all; spacefill off; wireframe; select atomno=4174; label protein; It's like Tcl, with lots of internal syntax handled by the individual commands. For example, "select atomno=4174" takes a full expression, like select atomno >= 195 and atomno <= 277 More details at http://jmol.sourceforge.net/docs/JmolUserGuide/ch04.html . The only way to tell that it works, in Python and without using Chime, is to re-write command interpreter that understands the script syntax. Andrew Dalke says that he tried something like that back in the 1990s, and while it's possible, it is not easy. When Andrew says things like that, you can bet money that it is very, very hard, because he does seemingly impossible things for fun over breakfast. Indeed, I wrote him hoping he would have scripts lying around that already do this ... He says that, these days, the best solution would probably be some in-browser Javascript code that drives Chime and checks if there's an error, but this is also not a job for somebody who is learning how to program, and iff it's less than several dozen/100 scripts, then really this is best done manually, unless the person enjoys programming. If you want to write him and ask him more questions, his contact page is at http://www.dalkescientific.com/contact.html He's very friendly, as well as being a very good friend of mine. Laura Creighton -- https://mail.python.org/mailman/listinfo/python-list
