[Modeler] Question about this alignment
Hello,
I have generated several protein models with modeller, However, for the alignment shown before, I didn't suceed. What am I missing?
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------------------------*
Thanks, Hoffmann
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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
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Hoffmann -
Modeller Caretaker