[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] [Modeler] Question about this alignment

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
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage