Answers.Body: <p>You can use <a href="https://www.cgl.ucsf.edu/chimerax/" rel="nofollow noreferrer">ChimeraX</a>.</p>
  <ol>
  <li>Open your glycans and your protein pdb files as different models, then move the models of your glycans until they are near the residues you want (in the Toolbar: <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mousemodes.html" rel="nofollow noreferrer">Right Mouse</a> -&gt; Move Model).</li>
  <li>Then use <a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html" rel="nofollow noreferrer"><code>combine</code></a> to combine one of your glycan model with the protein</li>
  <li>Finally Use Tools -&gt; Structure Editing -&gt; Build Structure and its <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds" rel="nofollow noreferrer">Adjust Bonds</a> menu to add covalent bonds. You can also add or delete atoms this way.</li>
  </ol>
  <p>This is a straightforward but complicated and tedious way of doing this, and it will give you unideal structures. There should be an equivalent way to proceed using PyMol. For a more automatized way I can only recommend having a look at <a href="https://www.pyrosetta.org/" rel="nofollow noreferrer">PyRosetta</a>. There is a <a href="https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb" rel="nofollow noreferrer">Jupyter Notebook tutorial about adding glycosylation</a>.</p>
  <p>There may be other tools out there for doing this, like <a href="https://software.acellera.com/docs/stable/moleculekit/index.html" rel="nofollow noreferrer">MoleculeKit</a>, but I'm less aware of them. A nasty solution would be to cut your protein in smaller pieces, glycosylate each part with CHARMM-GUI, then reassemble them.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-05T12:20:12.137Z
Answers.LastActivityDate: 2022-03-05T12:20:12.137Z
Answers.UserDisplayName: O.Laprevote
Answers.Body: <p><em>answer from @coot, converted from comments (please edit this answer to improve it if you can):</em></p>
  <p>Manual model building is a common thing in structural biology. Usually, Coot is used.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-02T22:52:21.947Z
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Answers.UserDisplayName: gringer
Body: <p>I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM.</p>
  <p>How can I attach the N and O-glycans onto each protein residue with software? In PyMol, I am stuck at loading up the protein PDB file and glycan file together, but I don't know how to put the two elements together. Are there any commands I can use? or tutorial resources I can take a look at? I'm open to trying other platforms.</p>
  <p>I've tried glycan modelling webtools (GLYCAM, CHARMM-GUI) but they can't seem to process my large glycoprotein - leading to errors or extended waiting times which also end in failure.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-02T03:32:20.890Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <protein-structure><pymol><modelling>
Title: How do I build a glycosylated protein from PDB files manually?
ThreadText: # How do I build a glycosylated protein from PDB files manually?
  
  (Asked by: username_0 on 2022-02-02)
  
  I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM.
  
  How can I attach the N and O-glycans onto each protein residue with software? In PyMol, I am stuck at loading up the protein PDB file and glycan file together, but I don't know how to put the two elements together. Are there any commands I can use? or tutorial resources I can take a look at? I'm open to trying other platforms.
  
  I've tried glycan modelling webtools (GLYCAM, CHARMM-GUI) but they can't seem to process my large glycoprotein - leading to errors or extended waiting times which also end in failure.
  
  **Tags:** protein-structure, pymol, modelling
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2022-03-05. Score: 2
  
  You can use [ChimeraX](https://www.cgl.ucsf.edu/chimerax/).
  
  1. Open your glycans and your protein pdb files as different models, then move the models of your glycans until they are near the residues you want (in the Toolbar: [Right Mouse](https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mousemodes.html) -> Move Model).
  2. Then use [`combine`](https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html) to combine one of your glycan model with the protein
  3. Finally Use Tools -> Structure Editing -> Build Structure and its [Adjust Bonds](https://www.cgl.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds) menu to add covalent bonds. You can also add or delete atoms this way.
  
  This is a straightforward but complicated and tedious way of doing this, and it will give you unideal structures. There should be an equivalent way to proceed using PyMol. For a more automatized way I can only recommend having a look at [PyRosetta](https://www.pyrosetta.org/). There is a [Jupyter Notebook tutorial about adding glycosylation](https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb).
  
  There may be other tools out there for doing this, like [MoleculeKit](https://software.acellera.com/docs/stable/moleculekit/index.html), but I'm less aware of them. A nasty solution would be to cut your protein in smaller pieces, glycosylate each part with CHARMM-GUI, then reassemble them.
  
  
  ---
  
  ### Answer by username_3 on 2022-02-02. Score: 1
  
  *answer from @coot, converted from comments (please edit this answer to improve it if you can):*
  
  Manual model building is a common thing in structural biology. Usually, Coot is used.
  
  
  ---
  
  