Dear sir,

I have 100 pdb files. named as output.1.pdb to output.100.pdb

what i do manually for clustering is as follows

1. select 100 pdbs -> open in chimera -> golto File -> save PDB.. -> Save Multiple Models as PDB File (renamed as all.pdb)

2. open chimera -> goto Tools -> MD/Ensemble Analysis -> MD Movie

3. in Get Ensemble Info dialogue box set -> Trajectory format : PDB

PDB frames contained in: single file

Browse to select File <all.pdb>

Use frames first through last

4. on click OK, a dialogue box pops out, MD Movie: PDB trajectory from all.pdb, in which, goto Analysis -> Cluster...

5.. on click Cluster, a dialogue box pops out, Get Clustering Parameters, in which I set Cluster trajectory as:

Starting frame: 1

step size: 1

Ending frame: 100

Cluster based on current selection, if any: true

Ignore solvent and non metal ions: true

Ignore hydrogens: true

Ignore metal ions: alkali

6. on click OK, after some RMSD calculation, i get the Clustering result, which I save to a text file <cluster>

Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard.

Thanks & Regards,

Subhrangshu Das

Junior Research Fellow, CSIR-IICB

Department of Structural Biology & Bioinformatics

Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091
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