Temperature color schemes

From Proteopedia

proteopedia linkproteopedia link

Fixed vs. Relative

Jmol offers two methods for coloring by temperature value. (For an introduction to the temperature value or B factor, please see Temperature value.)

Color Mapping to Temperature Values

SAT colors button	Jmol command	Blue	White	Red
temperature, fixed	color fixedTemperature	0	50	100
temperature, relative	color relativeTemperature*	minimum value	midpoint**	maximum value

*The relativeTemperature color scheme is the same as the temperature color scheme.
**Midpoint between the minimum and maximum temperature values, that is, min + ((max - min)/2).

Examples

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Resolution, PDB ID	Temperature values
	Min	Av	Rel White	Max
1cbn	2	5	11	20
2a4x	6	18	--	84
1io1	4	29	36	68
1uwb	10	67	54	100
3a8n	4	107	105	203
3lvh	50	103	--	328

Temperature of an atom is reported in the hover report (touch the atom, don't click).

Other examples:

• 2zqp 6.0 Å Temperature min/av/max: 328/328/328. Fixed is red; relative is white.
• 1bdx 6.0 Å Temperature min/av/max: 30/30/30. Fixed is light blue; relative is white.
• 1qd7 5.5 Å Temperature min/av/max: 0.0/19/102. Fixed & relative seem identical.

Jmol Scripts

The Jmol scripts used by the Temperature 0-10 and Add 10 buttons are:

• TempRangeReset.spt
• TempRangeStep.spt

These scripts require that the main script below be run beforehand.

The following Jmol script produces the above scenes, after loading any PDB file. After running this script, you enter the command "echo pdbID" to display the PDB ID in the upper left. When pasting this script into the Jmol Console (Jmol 11.8 used in Proteopedia in June, 2011), the semicolons were required in order for the echo commands to work properly.

select all;
cartoon off;
spacefill off;
wireframe 0.2 only;
background black;
ssbonds off;
color fixedTemperature;

hover Temp=%t, %n %R, Chain=%c, Element=%e(%a);
# Example: Temp=50.00, HOH 671, Chain=A, Element=O(O)

~tempmax = {*}.temperature.max;
~tempav = {*}.temperature;
~tempmin = {*}.temperature.min;

~tempmax = (~tempmax) % (0);
~tempav = (~tempav) % (0);
if (~tempmin < 1) {~tempmin = (~tempmin) % (1)};
else {~tempmin = (~tempmin) % (0)};

set echo all;
font echo 15 sansserif;
color echo [x00ff00];

set echo echotr 100% 100%;
set echo echotr right;
~report = "Temperature/B values:|Max " + @~tempmax ;
~report += "|Av " + @~tempav + "|Min " + @~tempmin;
echo @~report;

set echo echobl 0% 0%;
echo Fixed;

set echo echotrange 0% 8%;
echo All Atoms

set echo echotl 0% 100%;