Comments (3)
Hi !
-sr
is for calculating the RMSD matrix (used for the clustering) and -sa
is the selection for the alignment of the trajectory. So this is a good question because depending the alignment of the trajectory, your will observe very different things.
- If you use
-sa "resname LIG" -sr "resname LIG"
you will aligned the trajectory on the ligand and compute the trajectory on the ligand. It means that you will cluster your trajectory based on the atomic fluctuations of the ligand. - But if you use
-sa "backbone" -sr "resname LIG"
, you keep the alignement on the protein and you will cluster on the ligand pose. This could be a bias if you just want to cluster the differents conformation of your ligand, but it will be more accurate for ligand pose. Because the ligand position will be different if your take as reference the protein.
To summary:
- Atomic fluctuation of the ligand (local fluctuation, fragment fluctuation) -> Alignment on the ligand
-sa "resname LIG" -sr "resname LIG"
- How the ligand move in the protein -> Alignment on the protein
-sa "backbone" -sr "resname LIG"
Best regards,
Thibault.
from ttclust.
Hi !
-sr
is for calculating the RMSD matrix (used for the clustering) and-sa
is the selection for the alignment of the trajectory. So this is a good question because depending the alignment of the trajectory, your will observe very different things.
- If you use
-sa "resname LIG" -sr "resname LIG"
you will aligned the trajectory on the ligand and compute the trajectory on the ligand. It means that you will cluster your trajectory based on the atomic fluctuations of the ligand.- But if you use
-sa "backbone" -sr "resname LIG"
, you keep the alignement on the protein and you will cluster on the ligand pose. This could be a bias if you just want to cluster the differents conformation of your ligand, but it will be more accurate for ligand pose. Because the ligand position will be different if your take as reference the protein.To summary:
- Atomic fluctuation of the ligand (local fluctuation, fragment fluctuation) -> Alignment on the ligand
-sa "resname LIG" -sr "resname LIG"
- How the ligand move in the protein -> Alignment on the protein
-sa "backbone" -sr "resname LIG"
Best regards,
Thibault.
Thank you so much for the clarification and for that very useful tool :)
from ttclust.
You're welcome :)
Feel free to open a ticket again if you have any issues.
from ttclust.
Related Issues (20)
- File name size HOT 4
- problem in clustering MDS when the protein moves out from one edge of water box while applying periodic boundary conditions HOT 2
- Which version? HOT 1
- Clustering with only .pdb file (without .xtc file) HOT 1
- what is the unit of RMSD in the log file ? HOT 1
- Using TTClust on Google Colab HOT 7
- The representative frame HOT 4
- ttclust.py:726: ClusterWarning: scipy.cluster: The symmetric non-negative hollow observation matrix looks suspiciously like an uncondensed distance matrix HOT 1
- ValueError: xyz must be shape (Any, 2108, 3) I need a help for this HOT 1
- ValueError: 'c' argument HOT 4
- selection of heavy atoms of a ligand HOT 1
- FileNotFoundError: [Errno 2] No such file or directory: 'D:\\CLOUDS\\GoogleDrive\\WORK\\Perso\\DEV\\ttclust\\examples' HOT 2
- can i use a trajectory and align it to the same protein structure saved in another pdb file?
- Handling PBC
- Clustering of host guest systems HOT 2
- Saving all frames belonging to a cluster HOT 2
- RMSD as an input
- ValueError: invalid literal for int() with base 10: 'auto'
- Replotting the graphs
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