7.    Getting alternate conformations into O.

In the .ins file, you've gone to all that trouble setting up the alternate conformations using the PART command...

Well, here's where all that time and effort figuring things out seem like they're wasted...don't worry, you'll put all that knowledge to good use again...you'll have to do all it again after O!  But for now, getting those alternate conformations into O is the challenge at hand...

In Shelxpro, use option [O].  This sets up your .pdb file so that O can read it and display the alternate conformations, albeit with altered residue numbers:

So, Shelxpro takes the .pdb file that Shelx has output after refinement (in this case, ma190.pdb),

and it creates a new file, in this case temp_o.pdb, with the new residue, having its residue number offset by 1000 from the original.  Note that the coordinates for all the atoms in the residue that are not part of the alternate conformation are simply copied exactly.

Now, this temp_o.pdb can be read directly into O.  The alternate conformation will look like this:

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