I want to cluster multiple pdb files with respect to one reference pdb. I have to use Align > all this to *Ca in Pymol. However, how could i do this via scripting in Pymol? As I have multiple sets of pdb files with their own reference pdb files. Is it possible to do the same in Python via Jupyter Notebook in Pymol?
Within PyMol, you can either use PyMol scripting or python scripts as documented in the PyMol wiki: https://pymolwiki.org/index.php/Main_Page
Check out the script library for examples: https://pymolwiki.org/index.php/Category:Script_Library
You can also integrate pymol into your python scripts via the PyMOL API - there are various tutorials available on the internet, e.g. http://www.herongyang.com/Molecule/PyMol-Python-API.html
Biopython also provides a library of computational tools for handling Biomolecular data in python.
Also, depending on the level of similarity between the protein you align, you might want to use different command: align does a 3D-superposition based on a sequence alignment, while for more distantly related protein, a sequence-independent 3D alignment may give you better results. See my answers to these question:
https://www.researchgate.net/post/How_can_I_calculate_RMSD_between_two_ligands_crystal_and_docked
https://www.researchgate.net/post/The_mathematics_or_details_underlying_align_for_a_Click-button_way_in_GUI_interface_of_PyMOL
Example script that demonstrates how to align and cluster multiple PDB files with respect to a reference PDB file using PyMOL and Python:
```python
import pymol
# Start PyMOL
pymol.finish_launching(['pymol', '-qc'])
# Load the reference PDB file
pymol.cmd.load('reference.pdb', 'reference')
# Iterate over the list of PDB files to align and cluster
pdb_files = ['file1.pdb', 'file2.pdb', 'file3.pdb']
for pdb_file in pdb_files:
# Load the current PDB file
pymol.cmd.load(pdb_file, 'current')
# Align all atoms to the reference
pymol.cmd.align('current', 'reference')
# Cluster the aligned structure based on CA atoms
pymol.cmd.cluster('current', cutoff=3.0, selection='name CA')
# Save the aligned and clustered structure
pymol.cmd.save('aligned_clustered_' + pdb_file, 'current')
# Delete the current structure from the PyMOL session
pymol.cmd.delete('current')
# Quit PyMOL
pymol.cmd.quit()
```
In this example, you would replace `'reference.pdb'` with the path to your reference PDB file. Similarly, update `'file1.pdb'`, `'file2.pdb'`, and `'file3.pdb'` with the paths to your own PDB files.
The script iterates over each PDB file, loading it into PyMOL as the `'current'` object. It then aligns the `'current'` structure to the `'reference'` structure using the `align()` function. The alignment is performed on all atoms.
After the alignment, the script clusters the aligned structure based on CA atoms using the `cluster()` function. The `cutoff` parameter specifies the clustering distance threshold.
Hope it helps
- Badges
- Science method
- Similar topics
- Biological Science
- Histology
- Staining