[Chimera-users] Lost hydrogens when saving mol2 file

Varela, Lawrence Rocco Rocco.Varela at ucsf.edu
Wed Jun 23 14:36:16 PDT 2010

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 combined MOLECULE section without loosing any hydrogen atoms?

Thanks :-)


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