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Create PDB for heterodimer

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Create PDB for heterodimer


I am trying to reproduce results on designing of a prion dimer 1I4M from a paper ( ). I downloaded the PDB file from RCSB but it only includes a single chain representing the asymmetric unit. It doesn't look like I'm able to download the biological assembly and I'm wondering if it's possible to construct a PDB file easily in PyRosetta (or if I have to go to the full Rosetta I can do that). Alternatively I wonder if I'm able to simply copy the lines of the PDB and change the chain to B.


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Mon, 2013-08-05 19:11

I was able to download the biounit from by clicking on the "Download Files" link on the right, and then selecting "Biological Assembly (gz) (A+S)" from the drop-down menu. Granted, when unzipped and opened in Pymol, only the single asymmetric unit showed up. That's because biounits are typically represented as multi-model PDBs. If you open the PDB file in a text editor you should see enough residues for two chains, and you can get Pymol to display both of them by turning on Movie->Show All States

The other option to get crystallographic symmetry partners is to use the symexp Pymol command ( With the regular 1I4M pdb, something like "symexp sym, 1I4M, resi 156, cutoff=4" creates a new object with the symmetric partner, you can then save that as a PDB, and use a text editor to combine the two files.

In both cases, a bit of text editing may be required of the combined PDB. Specifically, you may want to rename the chain for the second partner, and remove the MODEL/ENDMDL lines. (Though I don't think either is strictly necessary for Rosetta to read the PDB in.)

There's ways to create a symmetric copy in Rosetta, and even to work with things symmetrically, but if this is a one-off and you don't want to preserve the symmetry, setting that up may be a bit more effort than just using PyMol & text editing to make the symmetric copy.

Tue, 2013-08-06 11:18