Ben,
thanks for suggestions!
The problem was in the charm-like naming of the Histidine residues in the input.pdb ( so its produce mismatch). Does it possible to make some aliases for HIS HSP HSE HSD (to His in sequence entry) as well as other titrable residues ?
James
2013/6/24 Modeller Caretaker modeller-care@salilab.org
> On 6/24/13 1:50 AM, James Starlight wrote: > >> _modeller.**SequenceMismatchError: get_ran_648E> Alignment sequence not >> found in PDB file: 1 ./input.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). >> >> >> How I could fix it ? >> > > Did you try doing what the error suggests? You didn't include input.pdb, > so I can't be sure, but it's quite possible that it doesn't have a chain > with no ID (as you specified in your alignment) but that it has an "A" > chain. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/**listinfo/modeller_usagehttp://salilab.org/mailman/listinfo/modeller_usage >