Hoffmann wrote: > I have generated several protein models with modeller, > However, for the alignment shown before, I didn't > suceed. What am I missing?
What error message did you get?
> structureX:1dkr:167:A:316:A:PDB::0.00:0.00 > DIVIVSPDHGGVTRARKLADRLKAPIAIIDKRXXXXXXXXXMNIVGNIEGKTAILIDDIIDTA----GTITLAANALVENGAKEVYACCT-HPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLFS* >> P1;pep > sequence::::::SEQ::0.00:0.00 > ------------------------------------AVADKRPRGRPRKHS-VISGQDFIEGGWVGWPEARQLAAALCQRRIP-CSVCLTKAVELGAPTDAFWLDPD-GVHCPLVPLRQRPTQRPVTLVSV------------------------*
You seem to have introduced a whole bunch of X residues in your alignment. These will only match UNK residues in PDB, and I don't see any UNK residues in 1dkr.
Ben Webb, Modeller Caretaker