Re: [Jmol-users] Can Jmol get the molecule in 3D (Was: loading jmol file from open babel)

Tue, 13 Feb 2007 12:13:26 -0800

I know this was from a while ago, but I just got around to trying it all out. Also I hope I'm not starting another war with the hydrogen thing :) . Personally i'm happy with Jmol.

So I tried out ChemSketch but it's windoze only. I'm trying MarvinBean's "molconvert" but that has an error when run throught the web saying "line 73: exec: java not found". Which isn't true becasue jmol runs, also when I run it from the terminal it works. Anywho, I had a google but didn't really find anything. So just asking if anyone has any ideas for a 2D -> 3D mol file converter.

Thanks
Research Technician
Mass Spectrometry
   o The
  /
o Scripps
  \
   o Research
  /
o Institute


Angel Herraez wrote: 
I am opening two new threads for Paul questions in his last post to " loading jmol file from 
open babel"

On 29 Jan 2007 at 10:44, H. Paul Benton wrote:

[snip]
  
 To all the other uses I have one more question to ask "Can Jmol get the molecule it a 3D 
manner, so it looks at the bond angles?" 
    

Paul, what do you exactly mean? I guess your files may be 2D, then it's not Jmol fault. If the 
loaded file has 3D coordinates, Jmol will show it 3D. But sometimes models have only 2D, 
then there is nothing that can be done by Jmol.


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