On 7/18/11 7:22 AM, Greene, Brandon Lee wrote: > There are three inorganic residues in the first chain and one in the > second placed as "." in my ali file.
Your alignment file does not match the PDB. Modeller reads the residues sequentially, so what it will see is
- A chain amino acids - B chain amino acids - A chain ligands - B chain ligands
So your sequence should also be in this order (XXXXXX/XXXXXX/.../.).
Alternatively, you can edit the PDB file to place the A chain ligands immediately after the A chain amino acids and leave your alignment unchanged.
> Using this structure and the template ali file to do the alignment (w/ > salign) I get poor alignment in the PAP file, but not in the PIR file??? > (P/---XXXX instead of P---/XXX in PAP).
Those two alignments are identical. Since neither gaps nor chain breaks are "real" residues, their relative ordering is irrelevant - it only matters which "real" residues (amino acids or ligands) they come between.
> "No aligned template residues for BLK residue; number of templates: 1 > Make sure that each BLK residue in your target sequence is aligned with > your templates..."
Just like it says, a BLK (".") residue in the target sequence must be aligned with a residue in the template. Usually this means you need a "." residue in the template in the same place as the "." in the target. You can't align a "." with a chain break or gap, because "." means to copy the aligned residue directly from the template to the target, so it needs a "real" residue to copy from.
Ben Webb, Modeller Caretaker