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
------------------------------------------------------------------------------
Got Input? Slashdot Needs You.
Take our quick survey online. Come on, we don't ask for help often.
Plus, you'll get a chance to win $100 to spend on ThinkGeek.
http://p.sf.net/sfu/slashdot-survey
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
