Hello Giannis,
> I make a simple protein viewer (with pdb code)
You are working with a web page + Jmol applet, right? Not the Jmol application.
> A. Is there a way to draw a pdb protein with Jmol without download pdb file.
> I would like to load the file from pdp.
To load directly from the PDB server, you use the command
load =1CRN;
But then you will need to use the signed applet (since the file is coming from
a different
server than the page and the applet, that is forced by Java security rules).
So,
jmolInitialize(".", true);
jmolApplet(400, "load =1CRN");
> B. How could I make a link with pdb code and open a popup window with this
> model in jmol
> I did it with http://chemapps.stolaf.edu/jmol/jmol.php
The popup system is explained there. I guess you knw how to do it.
There are other ways, but you need to investigate and test.
> but I don't know how show the model in cartoon mode and how I coloring the
> model...
It is explained there, you must add a parameter with the script:
<a target="_blank"
href="http://chemapps.stolaf.edu/jmol/jmol.php?&pdbid=1CRN&script=cartoon
only">see the
model</a>
> C. Is there a way to view my model in grey cartoon and coloring with other
> color (yellow for example)
> a specific positions in protein?
Of course.
select all; cartoon only; color cartoon gray; select 23-25; color cartoon
yellow; select all;
will color yellow residues 23, 24 and 25
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