VMD-L Mailing List

From: Scazzocchio, Claudio (c.scazzocchio_at_imperial.ac.uk)
Date: Sun Jul 17 2016 - 11:46:54 CDT

I am a relatively unsophisticated user of VMD. I encounter the following problem. While using the STAMP alignment, trying to structurally align a downloaded structure and with one modelled in I-Tasser, I get the following message:

The selection in sequence 5c3o was not completely composed of protein residues and can not be aligned by STAMP.
    while executing
"error "The selection in sequence [::SeqData::getName $sequenceID] was not completely composed of $sequenceType residues and can not be aligned by STAM..."

One of the sequences showed a whole load of question marks in the C-terminus, which I removed. It did not help

I had never had that problem before, even when the structure contains ligands.

I could superimpose easily both structures in Magic Fit in Swiss-PD-viewer.

Any ideas?,

Thanks

Claudio

Prof. Claudio Scazzocchio
Dept. of Microbiology,
Imperial College London
South Kensington Campus
Flowers Building
Armstrong Road
London SW7 2AZ.
UK
Tel int-44(0)20 7594 7409
c.scazzocchio_at_imperial.ac.uk