Hi Dan, Chimera assumes that sp3 nitrogens bonded only to sp3 carbons and/or hydrogens are positively charged at physiological pH. That means that their idatmType attribute is "N3+". If you actually do want to use the neutral species, you need to get the idatmType changed to "N3" before adding hydrogens. Here is some Python code that will change all selected nitrogens' idatmType to "N3": --- start code --- import chimera for a in chimera.selection.currentAtoms(): if a.element.name != "N": continue a.idatmType = "N3" --- end code --- You could either type that code into the IDLE interpreter (Tools-

General Controls->IDLE) or put it in a .py file and open that file with File...Open or with Chimera's command line.

--Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Dec 2, 2005, at 6:53 AM, Daniel Svozil wrote:

Hi all,

if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly?

Thanks Dan

-- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic

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