[Chimera-users] Writing a SINGLE pose (with ligand and protein) to a PDB file

[Edmund Marinelli]

Hello:  I used ViewDock to open a pdbqt file generated by use of AutoDock
Vina.  The ligand was shown in the graphics window.  Then I opened the
protein pdb file that was used in the docking experiment.  The ViewDock
dialog lists the poses obtained and I can select each and view the
resulting pose in the graphics window fine.  I opened the Model Pane.  I
selected from the list of models the first pose (#0.1) and the protein (#1)
in the list.  I assumed that saving these two into a file would give a file
that contained only the protein and the ligand bound as in the best pose .
I want to save the best pose as a pdb file wherein the protein and ligand
are present.  I gave a filename Test.pdb  .  Chimera returned the following
error message:  "You must provide a filename that contains either $name or
$number , which will be changed to the model name or model number
(respectively) in the final saved file name."  I do not understand what
this means.  I tried using the pose number and also the protein name but it
gave the same error. I don't understand what is meant by $name and $number
- what do they refer to ? What do I need to do to save a single pose
containing protein and the ligand to a unique file not containing other
poses?

The screenshot below is what I see:  Note that in the models list I
selected the best pose #0.1 and also the protein, which is at the bottom of
the list, hence it is not visible in the picture.  What is the filename
syntax that I need to use to save a pose with protein to a single PDB
file?  Stated more plainly: Can you give a viable example of what I need to
enter as a filename that will allow saving of the file?  Or am I going
about this all wrong?  Sorry for the verbose email.

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