[Chimera-users] RMSD calculation

Conrad Huang conrad at cgl.ucsf.edu
Tue Jul 10 12:27:51 PDT 2012

Here's a script that will print out the RMSD "distance" matrix for an 
ensemble (all models have exactly the same set of atoms).  To use, just run:

chimera --nogui --silent your_file.pdb dm.py > matrix

The output in file "matrix" should be N lines, each with N tab-separated 
floating point numbers, where N is the number of structures in 

Please let me know if that's what you're looking for.  Thanks.


On 7/10/12 11:32 AM, Austin B. Yongye wrote:
> Hi Dr. Huang,
> I would like to use the "nogui" mode.
> Thanks a lot!
> Austin-
> --- On Tue, 7/10/12, Conrad Huang <conrad at cgl.ucsf.edu> wrote:
>> From: Conrad Huang <conrad at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] RMSD calculation
>> To: "Austin B. Yongye" <ybausty at yahoo.com>
>> Cc: chimera-users at cgl.ucsf.edu
>> Date: Tuesday, July 10, 2012, 9:18 AM
>> Will you be running Chimera with a
>> graphical interface?  If so, then the
>> Ensemble Cluster tool already prints the RMSD matrix to the
>> Reply Log.
>> If you want to get the RMSD in "nogui" mode, please let us
>> know and we
>> can figure something out.
>> Conrad
>> On 7/10/12 7:57 AM, Austin B. Yongye wrote:
>>> Hello Chimera-developers/users:
>>> Does someone have a script that can perform pairwise
>> backbone RMSD
>>> calculations for a group of pdb structures in a file
>> and write out the
>>> RMSD matrix? This may already be implemented in the
>> clustering routine.
>>> Just need to get the RMSDs.
>>> Thanks,
>>> Austin-
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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