this is probably better:
Color atoms based on a crystallographic B-factor or "temperature" scale. Colors range from blue (least positional variability within the crystal) through white to red (most positional variability). Using a fixed scale allows direct comparison between two structures. Using a relative scale sets the blue-red range to match the range of varibility in the model itself.
I finally see what the connection is to temperature. Even perfectly ordered crystals will show higher positional variability at higher temperature due to vibrational effects. But that's not what this is used for. It's used for discriminating between atoms that are more tightly held in position (in the center of an enzyme or in a well-defined structure such as a beta-pleated sheet, for example) from those that are more loosely held in position (on the periphery or in a structurally transitional region, perhaps).
Bob
Miguel wrote:
documentation updated. How's this?
See
http://www.stolaf.edu/people/hansonr/jmol/docs/?search=temperature
color [temperature-mode]
Color atoms based on an absolute "temperature" scale from blue ("cold", less motion) to red ("hot", more motion) or using a relative "temperature" scale from blue ("coldest", least motion) to red ("hottest", most motion). This presumes crystallographic B-factor information.
where
[temperature-mode] is "fixedTemperature" or "relativeTemperature"
I think that's what we're talking about.
Essentially yes
color {object} temperature
Is RasMol/Chime compatible. The range is scaled to the min/max values that actually occur in the model. There is a difference from RasMol/Chime. The neutral color in RasMol/Chime is green. So RasMol/Chime go blue->green->red. Jmol goes blue->white->red
"relativeTemperature" is an alias for "temperature".
Q: Do you prefer 'scaledTemperature' instead of 'relativeTemperature'?
color {object} fixedTemperature
Will color things on an absolute scale from 0 to 100. 0 is always full blue. 50 is white 100 is full red.
Miguel
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