Re: [modeller_usage] Help with modeller 9.9 in windows
To: "Greene, Brandon Lee" <>
Subject: Re: [modeller_usage] Help with modeller 9.9 in windows
From: Modeller Caretaker <>
Date: Mon, 18 Jul 2011 12:21:16 -0700
Cc: "" <>
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.