This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there a way to save a full pdb file in PYMOL after uploading biological unit?

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
• 4,364 views • link
updated by tothepoint tothepoint • written by srdjanmasirevic2 • srdjanmasirevic2

1 answer

Try with save molecule as: new_name.pdb

or

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

• 0 views • link
written by tothepoint tothepoint

Log in to answer this question.

More posts like this