pyMODE-TASK usage¶
pyMODE-TASK is a PyMOL plugin and GUI for command line based MODE-TASK tool. It include all the functionality of the MODE-TASK.
PCA of a MD trajectory¶
1. Preparation of trajectory
Prepare the MD trajectory as described in the tutorial section of MODE-TASK. It involves removing waters and periodicity if any.
2. PCA
- Start the plugin from PyMOL, plugin –> pyMODE-TASK.
2. Locate the pyMODE-TASK directory in the configuration tab by clicking on button “pyMODE-TASK directory”. Browse to the directory and click ok.
- It should look something like this
4. Next go to the PCA tab. Read the trajectory, topology and reference PDB by clicking on the respective buttons. Next select the appropriate options and click on Run PCA. The results file will be saved in a folder within the output directory.
- If the run is successful you will see something like following
MDS and t-SNE¶
1. Read the trajectory, topology files by clicking on the respective buttons. Select the appropriate options under MDS options widget and click on Run MDS.
- Similarly, run the t-SNE.
Normal mode analysis (NMA)¶
- Set the configuration page to locate the pyMODE-TASK directory.
- Perform the coarse graining for large protein molecules.
3. Perform the coarse graining for second conformation of the protein. This is useful in case if you want to perform “Conformation/ Combination tool analysis” and “Mean square fluctuation”.
- Run NMA on each coarse grained PDB using a suitable cutoff.
- Run conformation / combination mode analysis. This require two PDB of different conformation.
- Run MSF. This requires decomposed ANM matrices for comparing the mean square fluctuation between 2 proteins.
- Get an assembly covariance for a specified chain of an asymmetric unit
- Generate mode animation for visualization. Afterward use the following command in VMD for visualization
vmd VISUALISE/VISUAL_1.pdb -e VISUALISE/VISUAL_ARROWS_1.txt