How to properly set the fields 5 of the second line in the .aln file?
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?
Thank you!
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".
The alignment file format is documented at https://salilab.org/modeller/9.24/manual/node497.html
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?
No.
Ben Webb, Modeller Caretaker
Thank you very much, Ben! I thought +33 and 33 were the same, but actually they are different. Now I used 33, and it is okay now.
(I am not sure why the post title got some weird words, =?gb18030?b?WkhBTkcgQ2hlbmc=?=, hope you do not mind)
------------------ Original ------------------ From: "Modeller Caretaker"<modeller-care@salilab.org>; Date: Thu, May 21, 2020 11:17 PM To: "ZHANG Cheng"<272699575@qq.com>;"modeller_usage"<modeller_usage@salilab.org>;
Subject: Re: [modeller_usage] How to properly set the fields 5 of the second line in the .aln file?
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".
The alignment file format is documented at https://salilab.org/modeller/9.24/manual/node497.html
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?
No.
Ben Webb, Modeller Caretaker
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ZHANG Cheng