Hi Sara Addinjg to what Rolf has replied,
> > The following script renders both atoms and bonds invisible. > > load http://pdb.rcsb.org/pdb/files/2ONA.pdb; > > color atoms TRANSLUCENT 300; Although "translucent" accepts several formats, the most intuitive is to use a number from 0 (opaque) to 1 (total translucent). "translucent" without a value gives 0.5, I think. So I'm not sure how your 300 is being interpreted, but I guess it's excessive. Please see details on http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#color As Rolf pointed aout, bonds inherit their color from atoms. So if you apply to atoms, you also apply to bonds unless you have issued a "color bonds" command. So the order seems to affect, though it is not quite the order. color atoms red; color bonds yellow; will work the same as color bonds yellow; color atoms red; and the same with translucency. Then you have color bonds none; to return to default inheritance from atoms. And any action applies just to the currently selected atoms (and to bonds between two currently selected atoms, unless you have set "set bondMode or") Hope this helps clarify your issue ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
