[modeller_usage] Re: Generating a model using multiple templates with different ligands

[Modeller Caretaker <>]

On 9/20/22 12:54 PM, Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - 
General Surg SF) via modeller_usage wrote:
> I have been trying to generate a model of the AhR using three different 
> templates with different ligands in each of them. When I submit the 
> script for the model building, I get the error below:
> 
> "_modeller.ModellerError: read_te_290E> Number of residues in the 
> alignment and pdb files are different:110 109 For alignment entry:13f1o_pasA"

The sequence in your alignment file must match that in the PDB file exactly.

The "236:A:+109:A" syntax in your alignment file header instructs 
Modeller to read residues from the PDB file starting at residue 236 in 
chain A, and ending once it hits the end of the file or has read 109 
residues, whichever happens first.

> I tried changing the number highlighted in the alignment file to 110, 
> but the same error appeared.

In that case you must have reached the end of the file.
See also https://salilab.org/modeller/FAQ.html#17

> Also, since I would like to consider the three ligands, is 
> that correct to add three dots at the end of the alignment and pap file? 

Yes, you would need three dots in your target sequence. Align each dot 
with a dot in the relevant template, and Modeller will copy the ligand 
from template to target.

>   _aln.pos   70        80        90       100       110
> 3f1o_pasA  QVVSGQYRMLAKHGGYVWLETQGTVIYN-----PQCIMCVNYVLSEIEK/.--
> 3h7w_pasA  QVVSGQYRMLAKHGGYVWLETQGTVIY------PQCIMCVNYVLSEIEK/.--
> 3h82_pasA  QVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK/.--
> AhR        ESGMIVFRLLTKNNRWTWVQSNARLLYK--NGRPDYIIVTQRPLTDEEG/...
>   _consrvd         * * *     *        *      *  *      *   *

This isn't right - you have asked Modeller to take the first ligand from 
all three templates (you will likely get a nonsensical ligand containing 
atoms from all three template ligands) and have not told it where to get 
the other two ligands from. You need to add gaps to your alignment so 
that the dots line up correctly, just as is done for amino acids. For 
example, if the first ligand should come from the first template, the 
second ligand from the second template, and the third ligand from the 
third template, your alignment would look like:

 >P1;3f1o_pasA
...
SEIEK/.--*

 >P1;3h7w_pasA
...
SEIEK/-.-*

 >P1;3h82_pasA
...
SEIEK/--.*

 >P1;AhR
...
TDEEG/...*

	Ben Webb, Modeller Caretaker
-- 
             https://salilab.org/modeller/
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