BIN ZHANG wrote:
> I was trying to add missing residues in pdb file according to the page:
>
> http://salilab.org/modeller/wiki/Missing%20residues
>
> But, one thing I don't understand is how can I get the "alignment.ali" file?
You have to create it manually. You can add the missing residues by
reading the REMARK lines in the PDB to figure out which ones are
missing, and then perhaps the SEQRES lines to figure out what the
residue types are.
> Aslo, it seems to me the command complete_pdb() can also do the job?
> http://salilab.org/modeller/manual/node403.html
> Is this true? If so, what's the difference between these 2?
No - complete_pdb does not add missing residues. It adds any missing
*atoms* for any residue - for example, if your input PDB contains only
CA coordinates, it will add (using internal coordinates) the rest of the
backbone and sidechain. But it won't add any residues that aren't in the
PDB in the first place.
Ben Webb, Modeller Caretaker
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