User:Eric Martz/Sandbox 19

1. The PDB file generated by PACUPP was uploaded to Proteopedia: Image:2j1n cavities fine small 3 5 20 24.pdb. (The published PDB file does not have the pseudoatoms added by PACUPP.)

2. Within PACUPP, the initial scene was modified (using PACUPP Peel and Extend commands), and then a state script was saved (write 2j1n.spt).

3. Using a plain text editor, the load command near the top of the state script was commented out by putting # before load.

4. The uploaded PACUPP PDB file was loaded into the present page using the SAT.

5. While in the SAT, the saved state script 2j1n.spt was dropped into JSmol.

6. The scene was saved, getting .

7. The previous scene was loaded in the SAT and the Jmol commands select protein; cartoon off; were issued manually, producing . Nothing was done to remove PACUPP's echo text that was at the top of scene #1. Apparently Proteopedia's SAT removed it automatically.

An alternative scene was saved showing . This scene could be loaded into the SAT, whereupon the top left echo text from PACUPP was gone, but THE SAVE SCENE TAB OF THE SAT BECAME UNRESPONSIVE. ???

The previous scenes #1-3 have pseudoatoms 3.0 Å in diameter (PACUPP cavity detail "fine"). For comparison, the van der Waals diameter of a carbon atom is 3.4 Å. The shapes of the channels are more detailed when the (PACUPP cavity detail "very fine"). Also revealed is a small buried cavity.