This atom specifier will select the nitrogen of the initial residue of each chain:

protein & @n & @/idatmType=N3+

It kind of sounds like you may already know your way around a script.  Let me know if you need more help with the scripting than the above.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 6, 2012, at 11:13 AM, michel dedeo wrote:

Hi,

I'm trying to measure the distance between the N-termini (or the first known residue) of a batch of dimeric proteins. The two proteins are different chains. I know how to do this by hand, but am exploring different ways to script it. It may be best to avoid using chimera entirely, but I thought I'd check to see if anyone knows a clever way to select the residue closest to the N-terminus when it's not residue #1.

Thanks for your help.

Michel
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