[Chimera-users] pseudo bonds in mol2 files

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 1 09:00:44 PDT 2010

Hi Francesco,
It would be helpful if you would attach the file or give the URL to find it -- however, I could find it by searching the Web.  Here is the tutorial URL in case anybody is interested:

We also recommend using "Help... Report a Bug" in the menu to report problems instead of mailing chimera-users.

However, maybe you weren't  sure it was a bug.  The problem is that some bonds (actually all the ring bonds whether aromatic or not, except one) are not being read correctly from the sustiva.mol2 file, and instead pseudobonds are created.  I don't know exactly what is causing the problem but I will report it.

If you open the PDB file from that tutorial, sustiva_new.pdb, it is read correctly and looks fine.

Chimera doesn't use extra lines to show double, triple, etc. bonds, but there is an option to show aromatic rings with  a solid or dashed circle, for example with the command "aromatic circle"
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 1, 2010, at 1:08 AM, Francesco Pietra wrote:

> I am confused about the meaning of pseudobonds for the aromatic
> portion of mol2 files. Typical example sustiva.mol2 in the
> antechamber-sustiva tutorial b4 of amber. I have the same
> representation for aromatic bonds in modified amino acids. In
> contrast, normal bonds from pdb files of the same molecules. Thanks
> for clarifying. francesco pietra

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