VMD-L Mailing List

From: Elijah Roberts (erobert3_at_scs.uiuc.edu)
Date: Wed Oct 22 2008 - 22:24:11 CDT

It looks from your email like you may be trying to align a FASTA
sequence to several structures using STAMP, which is a structural
alignment program. Is that accurate? If so, that will not work. Although
STAMP aligns the sequences of structures, it uses the 3D superposition
of the structures to do so. Without structural data STAMP cannot
function. You might want to instead try aligning the sequences from the
sequence and structures using CLUSTAL.

Elijah

Perreault, Roger Edward wrote:
> Hello VMD Users,
>
> I am attempting to align an imported FASTA sequence with several sequences from PDBs I also have loaded into Multiseq. I run a STAMP alignment with the default settings and the error message
>
>
> 'can't read 'SequenceIDtoMolID(122)': no such element in array'
>
>
>
> appears, though the numerical argument changes each time. Does this mean that there is a problem with my sequence? The problem does not occur if I attempt to align two of the template sequences.
>
>
>
> --Roger P.
>
> Middlebury, Vermont, USA
>
>