10 Oct
2012
10 Oct
'12
5:58 a.m.
Hello Yael,
On Wed, 2012-10-10 14:40 EDT, yael steuerman yaelsteu@mail.tau.ac.il wrote:
> Hello, > > I'm using thos PIR file: > >P1;2ks9 > structureX:2ks9:1 :A :364 : :::: > MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVNLAFAEAS ^ Your problem is right here. The structure does not include the methionine, but begins at residue 2, Asp. The SEQRES lines start at residue 1, but the structure does not and it is the sequence of the structure that must be in this alignment file. Also, residue number 364 in the coordinates is an Ala, but your sequence ends at residue Arg 353. So for the sequence you've given, the second line in your alignment file should be:
structureX:2ks9:2 :A :353 :::::
Cheers, Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821
robert.campbell@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc