Coloring by NMR Chemical Shift Perturbation using Chimera
November 28, 2018
UCSF Biophysics 204A tutorial
How to color the molecular surface of HSP90
by NMR chemical shift perturbation values using
UCSF Chimera version 1.13.1 (older versions will work).
Create a Chimera Attribute File
First convert our
chemical shift perturbation file that looks like
to a Chimera attribute file
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.
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
|Operation||Chimera menu entry
|Open HSP90 protein, PDB 1ah8
||File / Fetch by ID.
|Delete chain B
||Select / Chain / B and Actions / Atoms / Delete.
||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
||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...
|Operation||Chimera menu entry
|Gray background||Actions / Color / All Options
|Shadows and silhouette edges||Tools / Viewing Controls / Effects
|Reduce shininess||Tools / Viewing Controls / Shininess
|Residue labels and arrows||Tools / Depiction / 2D Labels or use a photo editor program.
There are some Chimera bugs that can cause trouble in this surface coloring procedure.
- Lowercase attribute name. The name we used in the attribute file was lowercase "csp" (short for
chemical shift perturbations). The attribute name should not start with uppercase. If the first letter
of the attribute name is capitalized the Chimera Render by Attribute tool will not show it, apparently
because it treats attributes that start with uppercase as constants.
of the attribute file format are given in the Chimera manual.
- Floating point values. The values in the attribute file should have a decimal point to
indicate they are floating point, for example "0.0" and not "0". Apparently the Chimera Render by Attribute
tool just looks at the value on the first residue to decide if the values are integer or floating point.
If it decides they are integer (no decimal point) then subsequent float values get rounded to integer.
- Tabs in attribute file. The format of the lines in the attribute file is "[tab]:resnum[tab]value".
The tabs cannot be replaced by spaces. Apparently this is to allow values that are strings with spaces
in them. Using a space instead of a tab will probably produce an error message.
- Moving models on Windows laptop with trackpad. On a Windows laptop with a trackpad Chimera uses
left click and drag to rotate, right click and drag (or scroll with 2-finger drag) to zoom and middle click
and drag to shift models left/right/up/down. Laptops don't usually have a way to emulate middle mouse.
So use Chimera menu Favorites / Preferences / Category Mouse and assign button 3 (right mouse) to be shift
(second column of table). Then shift can be done with right click (usually clicking in lower right corner
of Windows trackpad, and zoom can be done with a two-finger drag. On Mac laptops this is not needed since
Option and Command modifier keys can be held to emulate middle and right click, and also two and three finger
drag can do rotation and translation.