Brandon Hespenheide wrote:
There was a post a few days ago asking whether it was possible to
script Jmol to display straight lines from one 3D point to another 3D
point, and a reply asking for what use this would be. I would find
this functionality extremely useful for displaying/undisplaying
hydrogen bonds and hydrophobic interactions (which are defined by our
software). We currently offer these predefined selections in our PyMol
scripts (produced by our software), and I would like to make it
available on our web-based version of the software.
for displaying bonds I suggest to implement the RasMol bond <src>
<dest> + command (unbond), which is used to CONECT any two atoms,
allowing double bond wireframe rendering in PDB files (and may be, in
future Jmol versions, structure manipulations).
In general, any user-defined interaction could be
displayed this way (such as the small-world and contact-order networks
some people use to understand protein folding rates).
A draw command for any geometric object is an other construction
site, e.g.
draw line <ID> [x1,y1,z1] [x2,y2,z2]
Regards, Jan
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