[chimerax-users] Sequence specification for comparative modelling

[Eric Pettersen]

Hi David,
	This error message is really indicative that ChimeraX didn't prepare the input sequence for Modeller correctly -- the sequence doesn't match what Modeller perceives to be the order of the residues in the PDB file.  What you need to do is to use ChimeraX's Help→Report A Bug menu entry to file a bug report so I can see what version of ChimeraX you are running.  Please include the UniProt ID you used (I assume the PDB is 6opc).

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab 

> On Feb 17, 2021, at 1:53 PM, Haselbach,David <david.haselbach at imp.ac.at> wrote:
> 
> Hi, 
>  
> I am trying to make a comparative model using modeler. I downloaded my sequence from uniprot and a homolog protein from the pdb. I associated the sequence with the homologe and the alignment is okay however there are definitely regions where there is no match at all. So when I run modeler it fails with the following output:
>  
> get_ran_648E> Alignment sequence does not match that in PDB file: 1 ./6opc_1.pdb
> (You didn't specify the starting and ending residue numbers and
> chain IDs in the alignment, so Modeller tried to guess these from
> the PDB file.)
> Suggestion: put in the residue numbers and chain IDs (see the
> manual) and run again for more detailed diagnostics.
> You could also try running with allow_alternates=True to accept
> alternate one-letter code matches (e.g. B to N, Z to Q).
>  
> I have been trying to figure out how exactly to specify the chain IDs and residue numbers but I really didn’t get it.  May I ask you to provide an example please?
>  
> Best, 
>  
> David
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