text: user8598: 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?
  
  user6322: 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. 
  
original_text: 8598: <p>pdb code: <code>2obt</code></p>
  
  <p>The pdb file has a coordinates of a monomer.</p>
  
  <p>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:</p>
  
  <pre><code>set assembly, ""
  fetch 2obt, asu, async=0
  
  set assembly, "1"
  fetch 2obt, assembly1, async=0
  </code></pre>
  
  <p>After generating the functional dimer in  pymol under name <code>assembly1</code>, 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?</p>
   6322: <p>So on the GUI form of PyMOL on the right hand side you have a list of what is ambiguously called <code>objects</code> in PyMOL (models elsewhere), which can be enabled or disabled by clicking on their name.
  The name also has a <code>1/1</code> in green or similar. This indicates the state. In your case you have 2 states.</p>
  
  <p>To split a multistate object use</p>
  
  <pre><code>split_state prot_A
  </code></pre>
  
  <p>To combine two objects one uses the command</p>
  
  <pre><code>create new_name, prot_A or prot_B
  </code></pre>
  
  <p>Now, this has two caveats which if violated result in a nasty piece of modern art:</p>
  
  <ul>
  <li>if the chains, segment ids and residues are the same</li>
  <li>if you had two overlapping macromolecules</li>
  </ul>
  
  <p>To deal with the first, change the chain id on one of them.</p>
  
  <p>alter prot_B, chain='B'
     sort</p>
  
  <p>Segment identifier is a weird thing that most comp-biochem tools dislike, so I like to remove that</p>
  
  <p>alter prot_B, segi=''
     sort</p>
  
  <p>Now when you go to save your <code>new_name</code> 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 <code>new_name</code>.</p>
  
  <h2>Aligning two</h2>
  
  <p>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.</p>
  
  <pre><code>create twin, prot_B
  align twin, prot_A and chain B
  alter twin, chain='B'
  sort
  </code></pre>
  
  <h2>SDF files</h2>
  
  <p>If someone else has a multicompound sdf where the state is the header name, I strongly advise not to use <code>split_state</code>. Yes, the python pymol module (not the app) handles states in a really weird way, but states can be selected with <code>state 1</code> selection algebra and <code>state</code> is an argument for most commands that do not accept <code>state</code> selector. </p>
  