[Chimera-users] RMSD script

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 18 15:01:58 PST 2015


Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option.  That option is on by default.  If it was on and you didn’t select any atoms, it used all atoms.

> See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis"
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

More about selection:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Best,
Elaine

On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180 at nd.edu> wrote:

> Hi Elaine, thank you for your response. 
> 
> Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this?
> 
> Thank you very much,
> Ruthie
> 
> On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ruthie,
> If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie.  That tool has an all-by-all RMSD calculation option and you can save the results to a text file.  You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer.
> 
> I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files.  They have be named similarly with numbers but the numbers don’t have to be consecutive.  If loading the trajectory is successful,  the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map.  The RMSD can be calculated from all atoms or only specify ones that you have selected.  Then there is a button to “Save RMSDs” on the resulting map window.
> 
> See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis"
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Nov 18, 2015, at 9:38 AM, Ruth Nelson <Ruth.Nelson.180 at nd.edu> wrote:
> 
> > Hello,
> >
> > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel.
> >
> > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do.
> >
> > Thank you very much,
> > Ruthie
> >
> 
> 
> 
> 
> -- 
> Ruth Nelson, Graduate Student
> Department of Chemistry and Biochemistry
> University of Notre Dame
> rnelson9 at nd.edu




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