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<StructureSection load='' size='340' side='right' caption='' scene='99/995028/Pacupp/2'>
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 [https://www.umass.edu/microbio/chime/pacupp/command-details.pdf 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 <scene name='99/995028/Pacupp/1'>this scene #1</scene>.

7. The previous scene was loaded in the SAT and the Jmol commands ''select protein; cartoon off;'' were issued manually, producing <scene name='99/995028/Pacupp/2'>scene #2</scene>. 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 <scene name='99/995028/Pacupp/3'>solid protein chains, scene #3</scene>. <!--(The scene was re-loaded into the SAT and re-saved, which eliminated the text put at the top by PACUPP.)--> {{font color|red|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 &Aring; in diameter (PACUPP cavity detail "fine"). For comparison, the [[van der Waals diameter]] of a carbon atom is 3.4 &Aring;. The shapes of the channels are more detailed when the <scene name='99/995028/Pacupp_veryfine_small/1'>pseudoatoms are only 2.4 Angstroms in diameter</scene> (PACUPP cavity detail "very fine"). Also revealed is a '''{{font color|purple|small buried cavity}}'''.

</StructureSection>

== References ==
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