Hi Barb, We don't retain each daily build of Chimera, so I can't compare the two builds you mention. Nonetheless, the current daily build correctly protonates the imidazole rings I tested. and it shouldn't differ from the 9/21 build in this regard AFAIK. Is the imidazole- containing compound in a standard PDB file and if so can you tell me the ID code for it? If not, would it be possible for you to send me your structure file (just the compound part would be fine)? Also, what is it about the charge assignments that don't make sense? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 25, 2008, at 5:10 AM, Barbara Truitt wrote:

I have a compound which has an imidazole ring. When I Add Hydrogens, no hydrogens are added to the nitrogen atoms when I use the build from 9/21/08. The build from 9/4/08 adds the hydrogens, but some of the charge assignments in the resulting mol2 file don't make sense.

Barb Truitt _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users