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Orientation of exported molecule Log Out | Topics | Search
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WebMO Support Forum » Running WebMO Jobs » View Results » Orientation of exported molecule « Previous Next »

Author Message
Mark Iannone
Unregistered guest
Posted on Sunday, September 12, 2010 - 12:35 pm:   

When a job is run, the orientation of the molecule generally changes. When a molecule is exported, its orientation (e.g. in Jmol) is not the same as in the WebMO molecule viewer. (It appears to be the same for xyz, pdb or mol files.) Could you explain how to predict these changes?
Is there a way to export a molecule so that it will show up in a preferred orientation when opened in Jmol?
Thanks.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 160
Registered: 11-2006
Posted on Sunday, September 12, 2010 - 2:59 pm:   

There is really no way to predict the orientation from program to program, as the orientation is nor part of the file (xyz, pdb, mol) file format. Thus the initial orientation chosen by WebMO or Jmol is in some sense arbitrary. WebMO aligns the molecule according to the principal moments of inertia, but Jmol likely uses a different convention.

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