Hi everybody,
I have a little problem that probably is so simple to solve but I do not get
it...
I have a native structure plus some homology models, and I change the
temperature factor column of each pdb with DSSP predicted secondary
structures encoded from 1 to 8.
I first load the native structure like this (I call the applet in php):
$JMOL = "<script type=\"text/javascript\">
jmolInitialize(\"Jmol-12new\", true);
jmolSetAppletColor(\"white\");
var jmolcmds = [
\"load $NATIVE.pdb\",
\"set isosurfacePropertySmoothing FALSE\",
\"set appendNew true\",
\"frame all\",
\"display all\",
\"select 1.1; cartoon; set userColorScheme blue yellow red green
cyan orange magenta ghostwhite; set propertyColorScheme 'user'; color
property temperature\"
];
jmolApplet([580,580], jmolcmds.join(\"; \"));
</script>";
and then I load each homology model upon clicking a checkbox, like this:
$JMOLb .= "<input type=\"checkbox\" id=\"id_$nmod\"
onClick='jmolScriptWait(\"load append $MODEL.pdb; select @{(_lastFrame)};
cartoon only; color property temperature; frame all;\");
document.getElementById(\"id_$nmod\").disabled=true'>";
Like this I have no problem, each model is correctly colored by secondary
structure. But DSSP might crash with a native structure or a model; in the
former case I want to load the native structure without the temperature
factor changed, as a reference, but coloring it all in white and with an
echo saying DSSP has failed:
$JMOL = "<script type=\"text/javascript\">
jmolInitialize(\"Jmol-12new\", true);
jmolSetAppletColor(\"white\");
var jmolcmds = [
\"load $NATIVE.pdb\",
\"set isosurfacePropertySmoothing FALSE\",
\"set appendNew true\",
\"frame all\",
\"display all\",
\"select 1.1; cartoon; color white\",
\"set userColorScheme blue yellow red green cyan orange magenta
ghostwhite; set propertyColorScheme 'user'\",
\"set echo top left; font echo 12 serif bolditalic; color echo
black; echo DSSP crashed with native structure $NATIVE|No secondary
structure color\"
];
jmolApplet([580,580], jmolcmds.join(\"; \"));
</script>";
It works properly until I load the homology models. They are all in blue
(the first color of the user color scheme). It seems like Jmol has taken the
temperature range using the native structure temperature values. Since I
have loaded the native structure with the temperature values unchanged, the
range of these values do not go from 1 to 8, they go from 0 to around 100.
Then I load the homology models and they are all in blue since their highest
value is 8 and falls in the first category if we count from 0 to around
100....
So I would need to color the native structure in white and the homology
models according to temperature values BUT FROM 1 TO 8, not using the range
of the native structure. How can I specify a range of temperature values,
like the PyMol: spectrum b, rainbow, minimum=1, maximum=8. I would need to
assign colors based on fixed temperature values, not from 0 to 100, but from
x to y. Any suggestions?
Thanks a lot!
Daniel
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