[Chimera-users] Normal to the plane of the aromatic ring at the centroid

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 15 16:48:01 PDT 2013

On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" <apande at albany.edu> wrote:

> How would I draw a normal to the plane of an aromatic ring, at its centroid?

Hi Ajay,
	There's not a 100% direct way in Chimera, but what you can do is this:

1) Define the plane of the aromatic ring using the Axes/Planes/Centroids tool.

2) Use that tool's Save button to save the plane info to a file.  The info will include the plane center and normal.

3) Create a "BILD"-format file defining an arrow (BILD format here:  BILD format).  The start of the arrow would be at the center of the plane and the end (arrowhead) at the center plus some multiple of the normal.  Since the normal is of length 1, maybe two or three times the normal would look okay.  Also, the parameter that determines the width of the arrowhead should probably be reduced from the default value (4 times the arrow width) unless you make the arrow length considerably longer.  Anyway, an example:

.arrow 16.692 32.583 17.432 16.583 31.740 17.959 0.1 0.2

which shows a normal to the aromatic six-member ring of the ligand in PDB 121P.  The plane info was:

plane name, center, normal, radius
plane: ( 16.692,  32.583,  17.432) (-0.109, -0.843,  0.527) 1.446

3) Open the BILD file with the "open" or the File-Open menu item.  Make sure the file name ends with ".bild".  If the structure is the only other open model (or has the lowest model number), the arrow will be oriented correctly relative to the structure.  Otherwise, you will either have to use an open command that also specifies that you want the BILD opened in the same model number as the structure (e.g. "open 5 myarrow.bild") or use the "transform as" button in the Model Panel to make the arrow have the same transformation matrix as the structure (which can also be accomplished with the matrixcopy command).


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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