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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?

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  • $\begingroup$ can we says that "after uploading the biological unit is not the right wording" ?? --> When loading mmCIF structure files, the assembly setting controls whether PyMOL loads the asymmetric unit (assembly="") or a biological unit (e.g. assembly="1"). Assembly identifiers in mmCIF files can be arbitrary strings, but usually are numeric and most files define at least assembly "1". I guess the biological unit is created applying same symmetry operator on the asymmetric unit (or am I wrong ??). Ok PymolWiki says loading, actually loads ..... $\endgroup$
    – pippo1980
    Aug 27, 2023 at 11:10

1 Answer 1

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So on the GUI form of PyMOL on the right hand side you have a list of what is ambiguously called objects in PyMOL (models elsewhere), which can be enabled or disabled by clicking on their name. The name also has a 1/1 in green or similar. This indicates the state. In your case you have 2 states.

To split a multistate object use

split_state prot_A

To combine two objects one uses the command

create new_name, prot_A or prot_B

Now, this has two caveats which if violated result in a nasty piece of modern art:

  • if the chains, segment ids and residues are the same
  • if you had two overlapping macromolecules

To deal with the first, change the chain id on one of them.

alter prot_B, chain='B' sort

Segment identifier is a weird thing that most comp-biochem tools dislike, so I like to remove that

alter prot_B, segi='' sort

Now when you go to save your new_name object, in the popup of the GUI you get a dropdown menu defaulted to enabled (visible objects that have not be clicked to be disabled). There you can choose new_name.

Aligning two

If someone that is in not the OP author has a template protein and needs to make a dimer of another based on that, the process is the same.

create twin, prot_B
align twin, prot_A and chain B
alter twin, chain='B'
sort

SDF files

If someone else has a multicompound sdf where the state is the header name, I strongly advise not to use split_state. Yes, the python pymol module (not the app) handles states in a really weird way, but states can be selected with state 1 selection algebra and state is an argument for most commands that do not accept state selector.

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