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Article ID: 428 - Last Modified:

When I try to align protein structures I get an error:

Problems occurred during the protein structure alignment.
The structures were not aligned

How do I proceed?

You should do the following:

1) Ensure that all the structures being aligned are included in the Workspace (In box checked) and not just highlighted (selected) in the Project Table.

2) Check that the structures being aligned are similar. The alignment code looks at secondary structure elements (SSE) for aligning two proteins, so there has to be at least some similarity in SSEs in order for the structures to be aligned.

3) In rare cases, it has been found that the alignment code does not align systems with multiple chains. In that case:

i) Use a subset of the two proteins for the alignment, using the 'Select' option in the alignment panel.

ii) Align the proteins from the command-line, using the following command:

$SCHRODINGER/utilities/structalign -force

iii) Superimpose the two proteins. In Tools → Superposition, you can use the ASL expression 'backbone' to superimpose based on the backbone, or 'a.pt CA' to superimpose based on C-alpha only.

Please note that using the default 'All' ASL expression, the program will align SSEs and at the same time minimize RMS deviation of the C-alphas, for which you will have to apply a residue-based ASL for the alignment (rather than atom based). For example, here the ASL 'a.pt CA' (for C-alpha alignment) fails, whereas the ASL 'backbone' would work for the same system.

Keywords: warnings, protein structure alignment, ASL, SSE , secondary structure elements , Maestro

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