[phenixbb] elbow.builder

William Scott wgscott at chemistry.ucsc.edu
Sun Jun 3 14:33:06 PDT 2007

Hi folks:

I've been playing around a bit with elbow.builder, and found the  


  elbow.builder --opt --smiles c1ccccc1

gives me a nice, flat, hexagonal benzene

  elbow.builder --gamess --smiles c1ccccc1

gives me a benzene that is slightly bent out of plane and has other  
small distortions with respect to 6-fold symmetry.

Is this a problem with elbow, a problem with gamess, or a Jahn-Teller  


Also, I noticed elbow.doc requires a mozilla or netscape executable.   
Since both of these are obsolete, maybe a firefox executable should  
be an option?  On OS X, "open" should open a URL in the user's  
favorite browser, but it doesn't seem to work right with Safari  
(which stupidly opens a Finder window of the directory containing the  
html file).   My workaround was to make a shell script called  
"mozilla" that invokes Camino:

#!/bin/zsh -f
/usr/bin/open -a Camino "$@"

HTH someone.



William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

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