[chimera-dev] structure analysis feature in UCSF Chimera

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 8 12:21:36 PDT 2008

Hi Serge,
	It is our intent to get planes (and centroids) in there as  
measurables after a few last improvements to axis support.  Hopefully  
soon but unfortunately there are a lot of demands on my time.  As a  
stopgap I've attached a script that measures atom/axis distances/ 
angles to a plane.  You select either 4 or 5 atoms (select the 3 plane  
atoms last) and running the script will report the distance/angle in  
the Reply Log.  It was relatively easy to write the script because  
Chimera has a built-in primitive for determining 3-point planes.  But  
work needs to be done to easily support 4+ point planes (currently the  
points need to be sorted into "clockwise" or "counter-clockwise" order  
-- don't ask!).
	Aside from selecting atom with the mouse, order can be guaranteed in  
an atom specifier by using '@' symbols to separate atoms rather than  
','.  So, the following command will select the atoms from left to  

sel :3.a at ne2@cg :6.a at ce2@ce1 at cg

whereas the following command wouldn't guarantee the selection order  
of the first two atoms or the last three:

sel :3.a at ne2,cg :6.a at ce2,ce1,cg


On Sep 5, 2008, at 9:11 AM, Serge Gorelsky wrote:

> Hello,
> would it be possible to add the two following features to the
> "Tools/Structure Analysis" menu of UCSF Chimera: the distance between
> atom A and a plane of other 3 atoms B,C,D ("the height of a trigonal
> pyramid with atoms B, C, D at the base ") and the angle between an
> axis (defined by atoms A and B) and the plane B-C-D ?
> Thank you very much in advance.
> -- 
> Best regards,
> Serge Gorelsky (a Chimera user since 2005)

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