Swiss model for virus

Question

[Rob]

Hi friends I created a SWISS-MODEL(here:https://swissmodel.expasy.org/) for spike/surface glycoprotein amino acid of Cov-2. I downloaded a fasta file (here: https://www.ncbi.nlm.nih.gov/sars-cov-2/) and used in in modeling.

I am learning how to use this website and I have some question: 1.where can I find the virus that is source of crystallized spike protein template for this model?

1. how should I know the positions for amino acid mutations in the RBD (RBD amino acid preferences for Sars-CoV-2 binding to the ACE2) in my Sars-CoV-2 isolate. If there is a mutation or not? like this supplementary image (Figure S3) https://ibb.co/N7QmQHX with this explanation:

Figure S3. Logo Plot Representation of Mutation Effects on Binding and Expression, Related to 
 Figure 3
        Letter height indicates preference of each site for individual amino acids with respect to ACE2 binding (height above the center line) or RBD expression (height
        below the center line). Blue letters indicate the unmutated SARS-CoV-2 amino acid, and, where applicable, green letters indicate differences found in SARS-
        CoV-1. Yellow highlights mark residues that contact ACE2 in the SARS-CoV-2 or SARS-CoV-1 crystal structures. See the STAR Methods for details of how the
        amino acid preferences are calculated from the experimental measurements.

in this paper: https://doi.org/10.1016/j.cell.2020.08.012

this is my model: https://ibb.co/jb4VXmB