<p>The backbone can be specified using a selector for the names of these, which are <code>N</code>, <code>CA</code> (Cα) and <code>C</code> (C-prime).</p>
<pre><code>out = pymol.cmd.align('foo and name N+CA+C and polymer', 'bar and name N+CA+C and polymer')
rmsd, n_atoms, n_cyles, n_rmsd_pre, n_atom_pre, score, n_res = out
</code></pre>
<p>If you do not wish the proteins to be moved you can use <code>rms_cur</code>, which is just the rmsd.</p>

CC BY-SA 4.0
2023-02-13T01:51:42.017Z
Thank you for your answer! It works well! however,i want to further learn related knowledge about pymol like this. Can you provide some web/cook book name?
chengyun zhang
CC BY-SA 4.0
2023-02-10T18:29:12.463Z
2023-02-10T18:29:12.463Z
Matteo Ferla
<p>i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD).I want to use the python code to use pymol to calculate the backchain RMSD. I know how to align them but don't know how to calculate the RMSD.</p>
<pre><code>import pymol2
with pymol2.PYMOL() as pymol:
    pymol.cmd.load('foo.pdb', 'foo')
    pymol.cmd.load('bar.pdb', 'bar')
    pymol.cmd.align('foo', 'bar')
    
</code></pre>

CC BY-SA 4.0
2023-02-09T10:00:58.040Z
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.
Community
<python><pymol>
calculate the backchain RMSD between two pdb files by pymol in Python
# calculate the backchain RMSD between two pdb files by pymol in Python

(Asked by: username_0 on 2023-02-09)

i have two protein pdb files and want to calculate the backchain RMSD between them. As far as I know the GUI of Pymol can use align to calculate the RMSD (but I don't know if it is the backchain RMSD).I want to use the python code to use pymol to calculate the backchain RMSD. I know how to align them but don't know how to calculate the RMSD.
import pymol2
with pymol2.PYMOL() as pymol:
    pymol.cmd.load('foo.pdb', 'foo')
    pymol.cmd.load('bar.pdb', 'bar')
    pymol.cmd.align('foo', 'bar')

**Tags:** python, pymol
> **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.  

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## 1 answers

### Answer by username_2 on 2023-02-10. Score: 2

The backbone can be specified using a selector for the names of these, which are N, CA (Cα) and C (C-prime).
out = pymol.cmd.align('foo and name N+CA+C and polymer', 'bar and name N+CA+C and polymer')
rmsd, n_atoms, n_cyles, n_rmsd_pre, n_atom_pre, score, n_res = out

If you do not wish the proteins to be moved you can use rms_cur, which is just the rmsd.

> **Comments:**
> **username_0**: Thank you for your answer! It works well! however,i want to further learn related knowledge about pymol like this. Can you provide some web/cook book name?  

---

