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Exporting homodimer's crosslinks for AlphaLink2 #566

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jimfeng9705 opened this issue Aug 21, 2024 · 5 comments
Open

Exporting homodimer's crosslinks for AlphaLink2 #566

jimfeng9705 opened this issue Aug 21, 2024 · 5 comments

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@jimfeng9705
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For a homodimeric protein with two identical sequences A and B, how can we export the intra-subunit crosslinks (A,A) and inter-subunit crosslinks (A, B)? I can only export intra-subunit crosslinks (A, A) using XiView.
@colin-combe
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colin-combe commented Aug 22, 2024 •
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HI,
you mean when using the AlphaLink2 export function?

cheers,
Colin

@colin-combe
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colin-combe commented Aug 22, 2024 •
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try right clicking on the protein and setting the AlphaLink stoichiometry attribute to 2
(just remembered how this worked)

@colin-combe
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try right clicking on the protein and setting the AlphaLink stoichiometry attribute to 2

@jimfeng9705 - did this work for you?

@jimfeng9705
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jimfeng9705 commented Sep 25, 2024 via email

@colin-combe
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Hi,

For a homodimer protein complex, after uploading a pdb structure, the exported crosslinks are different from those in direct export without uploading the pdb. I attached the files.

The exports from the 3d panel after a pdb file is uploaded have the crosslinks mappped onto the selected structure. The residue numbers are then with reference to the pdb file chain sequences.

The export from the alphalink export option has all the crosslinks with the residues given with reference to the search sequences.

Various thing scan make these different, but with everything working correctly it is expected behaviour that they'll probably differ. This is what you are seeing, right? (I.e. output differing from two different export functions, one from 3D panel, one from alphalink export ).

Things such as differences between search sequences and sequences of proteins in the 3d model can cause this.

If the sequences in the homodimer structure you uploaded are identical to the search sequences then there is more of a question about why they differ. If these sequences are the same, we can look into why the outputs differ if you want, it might be useful.

Are the search sequences and the model sequence identical? How would you summarise the differences btw output? Its not just different order or something like that? Give an example of a difference. (I know you sent the data and I could look into this myself but i don't have time for that at moment.)

Which way shall we export?

If you want to model in AlphaLink then use the AlphaLink export.

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@colin-combe @jimfeng9705