Temperature color schemes
From Proteopedia
(→Fixed vs. Relative) |
(→Examples) |
||
| Line 186: | Line 186: | ||
*[[1bdx]] 6.0 Å Temperature min/av/max: 30/30/30. Fixed is light blue; 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. | *[[1qd7]] 5.5 Å Temperature min/av/max: 0.0/19/102. Fixed & relative seem identical. | ||
| + | |||
| + | ==Jmol Script== | ||
| + | The following Jmol script produces the above scene, after loading any PDB file. After running this script, you enter the command "echo pdbID" to display the PDB ID in the upper left. | ||
| + | <pre> | ||
| + | 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%; | ||
| + | </pre> | ||
Revision as of 03:53, 27 June 2011
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 |
Blue |
White |
Red |
|
|---|---|---|---|---|
|
temperature, fixed |
color fixedTemperature |
0 |
50 |
100 |
|
temperature, relative |
color relativeTemperature* |
minimum |
unclear |
maximum |
*The relativeTemperature color scheme is the same as the temperature color scheme.
Examples
|
|
Resolution, PDB ID |
Temperature values |
|||
|---|---|---|---|---|
|
Min |
Av |
Rel. White |
Max |
|
|
2 |
5 |
11 |
20 |
|
|
4 |
29 |
36 |
68 |
|
|
10 |
67 |
54 |
100 |
|
|
4 |
107 |
105 |
203 |
|
|
50 |
103 |
-- |
328 |
|
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 Script
The following Jmol script produces the above scene, after loading any PDB file. After running this script, you enter the command "echo pdbID" to display the PDB ID in the upper left.
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%;
