# Avogadro is changing bonds from saved file

**URL:** <https://discuss.avogadro.cc/t/avogadro-is-changing-bonds-from-saved-file/206>\
**Category:** General Discussion\
**Created:** [September 21, 2011, 2:48pm UTC](https://discuss.avogadro.cc/t/avogadro-is-changing-bonds-from-saved-file/206 "2011-09-21T14:48:10Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![George\_Barbosa](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/g/f08c70/32.png) [@George\_Barbosa](https://discuss.avogadro.cc/u/George_Barbosa)\
**Post date:** [September 21, 2011, 2:48pm UTC](https://discuss.avogadro.cc/t/avogadro-is-changing-bonds-from-saved-file/206/1 "2011-09-21T14:48:10Z")

</div>

Hello, I’m a newbie at Avogadro. I drew a molecule derived from an amino  
acid, optimized its geometry with Avogadro, saved the file and closed it.  
But then when I opened it briefly later some bonds were changed. Actually  
this is happening all the time with the same bonds (single bonds in a  
benzene ring are being converted to double ones and vice-versa). I just want  
to keep the molecule as I draw it. Could someone please tell me how I will  
be able to do this?

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [September 21, 2011, 2:54pm UTC](https://discuss.avogadro.cc/t/avogadro-is-changing-bonds-from-saved-file/206/2 "2011-09-21T14:54:13Z")

</div>

On Sep 21, 2011, at 10:48 AM, George Barbosa wrote:

> Hello, I’m a newbie at Avogadro. I drew a molecule derived from an amino acid, optimized its geometry with Avogadro, saved the file and closed it. But then when I opened it briefly later some bonds were changed

Depending on the file format you used, bonding information may not be included. Avogadro uses CML as its native format, which will store bond orders. But if you save as a PDB or XYZ format, bond orders are not saved and Avogadro will have to work out the bond orders again.

Also, keep in mind that Avogadro attempts to re-center a molecule when opening – this may rotate the frame of reference so that atoms are not in the same place.

Hope that helps,  
-Geoff

* * *

Prof. Geoffrey Hutchison  
Department of Chemistry  
University of Pittsburgh  
tel: (412) 648-0492  
email: [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com)  
web: [http://hutchison.chem.pitt.edu/](http://hutchison.chem.pitt.edu/)