Re: [Jmol-users] color atoms property temperature range??

[Daniel C. <dan...@gm...>]

So what I would like to do is something like the following, which obviously
does not work:

$JMOL = "<script type=\"text/javascript\">
     jmolInitialize(\"Jmol-12new\", true);
     jmolSetAppletColor(\"white\");
     var jmolcmds = [
          \"load $ZIPtoUSE|$folder/$native.pdb\",
          \"set frank off; select all; hbonds off; spin off; wireframe off;
spacefill off; trace off; set ambient 40; set specpower 40; slab off;
ribbons off; cartoons off; label off; monitor off\",
          \"set showAxes true\",
          \"set appendNew true\",
          \"frame all\",
          \"display all\",
          \"select 1.1\",
          \"var MIN = {selected}.temperature.min\",
          \"var MAX = {selected}.temperature.max\",
          \"cartoon; set propertyColorScheme 'bwr'; color atoms property
temperature ABSOLUTE MIN MAX\",
          \"script Jmol-12new/myJMOLfunctions.spt\"
     ];
     jmolApplet([580,500], jmolcmds.join(\"; \"));
</script>";

for each model:
$JMOL .= "<input type=\"checkbox\" id=\"id_$nmod\"
onClick='jmolScriptWait(\"load append $ZIPtoUSE|$folder/$model; select
@{(_lastFrame)}; var MIN = {selected}.temperature.min; var MAX =
{selected}.temperature.max; cartoon only; color atoms property
temperature ABSOLUTE
MIN MAX; frame all; hide hidden;\")'>;


How should I do it? Thanks a lot,
Daniel








2011/7/28 Daniel Carbajo <dan...@gm...>

> Hello everyone,
> I have one little problem that had gone unnoticed until now. I have a Jmol
> window where I load one protein by default (a native structure) and a table
> next to it that gives the possibility to load many proteins (all of them
> models built by homology out of the native structure, so sharing the same
> sequence), and I color them all based on their temperature factor records
> (which I replace with other descriptors like solvent accessibilities, atom
> depth inside a cavity, burial indexes or protrusion indexes, for which I do
> not even now the range they span).
> If I load one protein at first it is colored correctly, but if the same
> protein is loaded in third position (the third protein loaded) for example,
> it is colored following the same pattern but with more pale colors.
> This makes me think that when I color the protein, the temperature factor
> ranges taken into account are not the ones of the protein itself, but of all
> the proteins loaded, how can I resolve this without using "temperature
> absolute *range*", since I do not know the range for some descriptors
> (they do not specify in the article)? I do it like this:
>
> $ZIPtoUSE-->zip file with the native structure plus the homology models
> $folder-->folder inside the zip file
> $native-->native structure, protein loaded by default
> $model-->homology model, proteins that can be appended
>
> $JMOL = "<script type=\"text/javascript\">
>      jmolInitialize(\"Jmol-12new\", true);
>      jmolSetAppletColor(\"white\");
>      var jmolcmds = [
>           \"load $ZIPtoUSE|$folder/$native.pdb\",
>           \"set frank off; select all; hbonds off; spin off; wireframe off;
> spacefill off; trace off; set ambient 40; set specpower 40; slab off;
> ribbons off; cartoons off; label off; monitor off\",
>           \"set showAxes true\",
>           \"set appendNew true\",
>           \"frame all\",
>           \"display all\",
>           \"select 1.1; cartoon; set propertyColorScheme 'bwr'; color atoms
> property temperature\",
>           \"script Jmol-12new/myJMOLfunctions.spt\"
>      ];
>      jmolApplet([580,500], jmolcmds.join(\"; \"));
> </script>";
>
> foreach model:
> $JMOL .= "<input type=\"checkbox\" id=\"id_$nmod\"
> onClick='jmolScriptWait(\"load append $ZIPtoUSE|$folder/$model; select
> @{(_lastFrame)}; cartoon only; color atoms property temperature; frame all;
> hide hidden;\")'>;
>
> If there is not a way I should investigate more and get the ranges for atom
> depth inside a cavity, burial indexes and protrusion indexes, I
> guess... Thanks a lot!
> Daniel
>
>