Re: [modeller_usage] No atoms were read from the specified input PDB file
To: <>
Subject: Re: [modeller_usage] No atoms were read from the specified input PDB file
From: Robert Campbell <>
Date: Wed, 10 Oct 2012 08:58:11 -0400
Hello Yael,
On Wed, 2012-10-10 14:40 EDT, yael steuerman <>
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
<> http://pldserver1.biochem.queensu.ca/~rlc