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 run in a terminal window, and an editor can be used to add the header lines saying it is a residue attribute.

      python < shifts.txt > shifts_attr.txt

Coloring HSP90 Surface

Spin movie
OperationChimera menu entry
Open HSP90 protein, PDB 1ah8 File / Fetch by ID.
Delete chain B Select / Chain / B and Actions / Atoms / Delete.
Show surface Actions / Surface / Show.
Read attribute file Tools / Structure Analysis / Define Attribute.
Color using attribute Tools / Structure Analysis / Render by Attribute.
Create color key on image Render by Attribute panel button Create Corresponding Color Key
Save image File / Save Image....
Save movie spinning 360 degrees Favorites / Command Line
"movie record ; turn y 1 360 ; wait 360 ; movie encode ~/Desktop/1ah8_csp.mp4"
Save Chimera session File / Save Session As...

Prettier Images

OperationChimera menu entry
Gray backgroundActions / Color / All Options
Shadows and silhouette edgesTools / Viewing Controls / Effects
Reduce shininessTools / Viewing Controls / Shininess
Residue labels and arrowsTools / Depiction / 2D Labels or use a photo editor program.