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.
"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.
Prof. Claudio Scazzocchio
Dept. of Microbiology,
Imperial College London
South Kensington Campus
London SW7 2AZ.
Tel int-44(0)20 7594 7409