[modeller_usage] How to properly set the fields 5 of the second line in the .aln file?
To: "=?gb18030?b?bW9kZWxsZXJfdXNhZ2U=?=" <>
Subject: [modeller_usage] How to properly set the fields 5 of the second line in the .aln file?
From: "=?gb18030?b?WkhBTkcgQ2hlbmc=?=" <>
Date: Thu, 21 May 2020 23:08:45 +0800
Cc: =?gb18030?b?1cKzzFFR?= <>
Feedback-id: webmail:qq.com:bgforeign:bgforeign11
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".
When it is changed to "1 :A:+31 :B", the same error occurred.
However, when only Chain B is modelled, "3 :B:+33 :B" can be run successfully.
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.
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?