[Chimera-users] Lost hydrogens when saving mol2 file

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 23 14:42:49 PDT 2010

Hi Rocco,
Doublecheck that the hydrogens are not merely undisplayed (for example, use the command "display" to display all atoms).  It might be that the smart initial display hides hydrogens.  I think it decides based on how many atoms are in the molecule, and when the molecules are combined rather than separate, it may go over that threshold.

If they really aren't there, please use "Help... Report a Bug" in the Chimera menu to report a bug,  providing enough information for us to reproduce the problem.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 23, 2010, at 2:36 PM, Varela, Lawrence Rocco wrote:

> I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera.  Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers.  Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option.  When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed.  How do a save multiple models in a combinedMOLECULE section without loosing any hydrogen atoms?
> Thanks :-)
> Rocco

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