How to get a pdb of the second chain of a homodimer using VMD?

Question

[mcleodcmm]

I have a pdb of one chain of a homodimer. How would I be able to also get a pdb for the other identical chain so that I can generate a psf?

Answer 1

[a.polo88]

It's strange that you have a pdb of an homodimer with the only one chain. the problem is that if you need a pdb of the second chain you must have the crystallographic coordinates. Are you sure that the determined structure contains only one chains? Have you read the reference?

Answer 2

[venu]

Will you please provide the pdb id, so that we can understand it more clearly to get a solution. Do BLAST with the other identical chain first. Then it will give an idea about the structure.

Answer 3

[Jiyao Wang]

Typically the other symmetric chain is defined by matrix. You can try to download PDB from NCBI MMDB. It usually output the coordinates of symmetric chains as well, e.g., change “format” to “PDB” and click “download” at https://www.ncbi.nlm.nih.gov/Structure/pdb/2POR.