Hello everyone:
I am working on a project with Jmol to show the surface of molecules.
The process is like this:
I have two PDB files, one is the protein data bank, and the other is the
binding site of the protein which is presented as standard PDB format.
I use this script to load the two into one view:
1. jmolInitialize("applet", "JmolApplet.jar");
2. jmolApplet(600, "load "+pocket+";load append "+pdb+";frame all;script
align_center.scr; center_frames;"+
3. "select 1.1; spacefill 50%; select 2.1; spacefill off;");
Now I want to add four jmolRadios to show the surface the two PDBs on or
off respective, the script is this:
4. jmolRadio("select 2.1; isosurface pdb_sur solvent;color blue; color
isosurface yellow;","pdb_surface", false); // set protein surface on
5. jmolRadio("isosurface pdb_sur off","pdb_sur_off",false); // set
protein surface off
6. jmolRadio("select 1.1; isosurface pocket_sur solvent; color isosurface
blue;","pocket_surface", false); // set pockets surface on
7. jmolRadio("isosurface pocket_sur off","pocket_sur_off",false); // set
pockets surface off
But the problem is that the script which show protein surface on( line
number 4) is not work when the radio button is pressed.
Please note the script "color blue" in line number 4, this is for testing
whether the protein molecule is selected, then when the radio button is pressed
the color of protein molecule do change to blue, it means the second PDB has
just been select. It is like that the script "isosurface pdb_sur solvent;" has
not been executed, this is crazy ?
On the contrary, the scripts which show pockets surface on and off ( line 6
and 7) is working very well, but there is nothing difference of substance
between the two part of scripts, why the first part (line 4) can not work ?
Another phenomena is that when I changed the script( line 4) to this:
4. jmolRadio("select all; isosurface pdb_sur solvent;color blue; color
isosurface yellow;","pdb_surface", false); // set protein surface on
only the surface of pockets appeared again, there is nothing surface of
protein can be seen.
I do not what to do to solve it, does anybody can help me?
Thanks very much and good luck!
best wishes
Zengming zhang，[email protected]
2009-04-22
Tel: +86-0571-86971772
Mobile:+86-13408688196
MSN: [email protected]
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