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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>