[chimera-dev] quartinary structure

[Thomas Goddard]

Hi Manning,

  We have a feature in our development version of Chimera that will make
the second half of th 1p7b ion channel.  But it is not released yet.

  Here is a way to do it with the currently distributed Chimera 1700.
It is not pretty.  First I looked at the PDB file in an editor to see
what matrix gives the position second copy.  Here it is.

REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000       92.84000            
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000      105.62000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000            

This means rotate about the z axis by 180 degrees and then translate
by (92.84, 105.62, 0).

  Here are the steps.

  1. Open 1p7b twice in the same Chimera.
  2. Use Favorites/Model Panel and click off the "active" switch by model 0.
     This will make the following move commands only act on model 1.
  3. Use Tools/Viewing Parameters/Rotation and set center of rotation method
     to fixed and set the rotation center to 0, 0, 0.  This is needed
     because the rotation done in the next step has to be about the origin
     of the coordinate system.
  4. Use Favorites/Command line and type the command "turn z 180".
  5. Type command "move x 92.84"
  6. Type command "move y 105.62".  If all went well you should now see
     the full ion channel.
  7. Switch back on the active switch for model 0 in the Model Panel.
  8. Switch the center of rotation method back to "center of models".

Of course you don't want to do this again next time you need to look at
the ion channel.  You can use File/Save Session As... to save the full
ion configuration.  If you want a single PDB file with the full channel
use the Chimera command "pdbrun cat > filename.pdb".  There is a
"Write PDB" button in Model Panel that can write both copies to a single
file in our development Chimera, but the ability to write multiple
copies to one file is not in the current release.

  I don't completely understand your question about "tagging residues".
You can select residues using Model Panel.  First click on the model
in the model panel list of models, then press "Sequence...", then
select residues in the sequence.  To select non-contiguous residues
use Select/Selection Mode/Append and then select them from the sequence
panel.  You can put labels on selected residues with Actions/Label.

	Tom