Is there a way to save a full pdb file in PYMOL after uploading biological unit?
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0
Entering edit mode
18 months ago

pdb code: 2obt

The pdb file has a coordinates of a monomer.

I have used following commands to generate an assembly, or in other words to upload one more biological unit so that the protein would be a dimer:

set assembly, ""
fetch 2obt, asu, async=0

set assembly, "1"
fetch 2obt, assembly1, async=0

After generating the functional dimer in pymol under name assembly1, I have an important issue that I cannot save a dimer structure in pdb file with dimer coordinates. Does anybody has an idea how to go around it or is it even possible to do that?

PYMOL Protein dimer • 1.7k views
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1
Entering edit mode
18 months ago
tothepoint ▴ 610

Try with save molecule as: new_name.pdb

or

copy and paste the coordinates in text editor like notepad++ and save as name.pdb

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