Coloring by NMR Chemical Shift Perturbation using Chimera

Tom Goddard
November 29, 2017
UCSF Biophysics 204A tutorial

How to color the molecular surface of HSP90 by NMR chemical shift perturbation values using UCSF Chimera version 1.12.

Create a Chimera Attribute File

First convert our chemical shift perturbation file that looks like

Assignment	CSP
V201N-H 	0.022
L56N-H 		0.052
D142N-H 	0.066
...
    

to a Chimera attribute file (documentation) that has residue number and chemical shift value and a minimal header like (note tabs are required):

#
#  Chemical shift perturbations for HSP90, PDB 1ah8.
#  Use this file to assign the attribute in Chimera with the Define Attribute tool.
#
attribute: csp
match mode: 1-to-1
recipient: residues
	:201	0.022
	:56	0.052
	:142	0.066
	...
    

The assignment in column 1 can be converted to a residue number with a Python script csp.py run in a terminal window, and an editor can be used to add the header lines saying it is a residue attribute.

      python csp.py < shifts.txt > shifts_attr.txt
    

Coloring HSP90 Surface

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