Re: [modeller_usage] How to properly set the fields 5 of the second line in the .aln file?

["ZHANG Cheng" <>]

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"<>;

Date: Thu, May 21, 2020 11:17 PM

To: "ZHANG Cheng"<>;"modeller_usage"<>;

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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