Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

[Eric M. <em...@mi...>]

Sometimes yes:

  * A prediction of structure from sequence vs. the X-ray structure.
    Example: SARS-CoV-2 ORF8 7jx6 vs. the top prediction in CASP14, by
    AlphaFold2:
      o download from
        https://predictioncenter.org/casp14/MODELS_PDB/T1064-D1/T1064TS427_1-D1.pdb
      o see all results at
        https://predictioncenter.org/casp14/results.cgi?view=tables&target=T1064-D1&model=1&groups_id=
  * One could homology model sequence A onto structure B, then compare
    structure of A (as the homology model) with structure B.

Sometimes no:

  * A new structure vs. the top structure-similarity hit from the PDB
    with a different sequence (e.g. found by Dali). For example,
    SARS-CoV-2 ORF8 7jx6, top Dali hit is 5a2f, sequence identity <10%,
    but the structures have the same fold, RMSD 3.2 Å for 88 residues
    out of ~100 total.
      o http://ekhidna2.biocenter.helsinki.fi/barcosel/tmp//7jx6a/7jx6A-25.html

On 2/27/21 1:25 PM, Robert Hanson via Jmol-users wrote:
> Eric, do the two proteins have the same sequence?
>