Re: [modeller_usage] How to properly set the fields 5 of the second line in the .aln file?
To: ZHANG Cheng <>, modeller_usage <>
Subject: Re: [modeller_usage] How to properly set the fields 5 of the second line in the .aln file?
From: Modeller Caretaker <>
Date: Thu, 21 May 2020 08:17:33 -0700
On 5/21/20 8:08 AM, ZHANG Cheng wrote:
I have a two-chain protein to model, Chain A and Chain B.
In the PDB file, the Chain B residues are numbered from 3-33, so only 31
residues appear in the PDB. When "1 :A:+33 :B" is used for the fields
3-6 in the second line of the .aln file, I got error: "Number of
residues in the alignment and pdb files are different".
Field #5 is either the number of the last residue to read, or +N (where
N is the total number of residues). So "+33" will tell Modeller to read
33 residues (unless it hits the end of the file first).
When it is changed to "1 :A:+31 :B", the same error occurred.
Nobody will be able to tell you why this is happening without being able
to see your alignment file and PDB.
So, it seems that, when Field 5 = n, it assumes that the last chain has
in total n residues, not the last residue is numberred as n.
This is not correct.
So how should I set the Field 5 number? Do I have to renumber the Chain
B residues in the PDB from 1 to 31?