Sorry for the title, it should read "color temperature with a user fixed
range", or something like that
2011/4/1 Daniel Carbajo <daniel.carb...@gmail.com>
> 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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