[Chimera-users] clustering models of a single pdb

[Subhrangshu Das]

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
*+919804938813*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200926/1a9805a5/attachment.html>