Re: [modeller_usage] Help with modeller 9.9 in windows

[Modeller Caretaker <>]

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
--
             http://www.salilab.org/modeller/
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