[Chimera-users] clustering models of a single pdb

[Subhrangshu Das]

Thank you Eric sir. It was very helpful. But what i finally need, is all
the members of the largest cluster. No while using *Ensemble Cluster *instead
of *MD Movie, *the saved output is only showing representative structure
from each cluster. Although in "Model Panel" (on click), the members of any
cluster is there, yet panel is not being saved into a text file.

On Mon, Sep 28, 2020 at 11:09 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Subhrangshu,
> You would need to be pretty good with Python to do this.  First, you would
> want to look at this: Very Basic Chimera Programming Primer
> <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> to
> get an idea of how to write a script for Chimera to process many data files.
> Second, scripting the MD Movie dialog is almost impossible, so I think you
> want to use the Ensemble Cluster dialog instead.  Your workflow would
> basically be:
>
> 1) Open 100 pdb files.
> 2) Delete the parts you don't want in the clustering calculation (e.g
> hydrogens)
> 3) Bring up a Ensemble Cluster dialog for your files.
> 4) Save the clustering
> 5) Close your files and the dialog and repeat as necessary
>
> Tips on the above:
>
> #2: There aren't commands that exactly match what the Movie dialog does.
>  "del solvent" and "del H" will delete solvent and hydrogens.  "del ions"
> will delete all ions, so if there are particular metals you would want to
> preserver, for instance magnesium, you would have to modify that to "del
> ions & ~ Mg".
>
> #3: You are going to need to bring up the dialog using Python code,
> because you will need a Python reference to the dialog.  The code for that
> is:
>
> from EnsembleMatch import EnsembleCluster
> d = EnsembleCluster(chimera.openModels.list(), "")
>
> #4: In order to save the clustering, you are going to have to replicate
> the code for _SaveClusteringInfo.Apply (which uses the dialog instance)
> found in EnsembleMatch/base.py, which is in <your Chimera
> installation>/share (or Chimera.app/Contents/Resources/share on a Mac).
>
> #5: Close the dialog with d.Quit()
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On Sep 25, 2020, at 12:40 PM, Subhrangshu Das <subhrangshu73das at gmail.com>
> wrote:
>
> 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*
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>

-- 
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*
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