[Chimera-users] Visualizing MDFF Runs in Chimera

[Elaine Meng]

Hi Joshua,
Unfortunately Chimera does not store separate attributes for different frames within a trajectory, so the only thing I can think of is to do the calculations “on the fly” with a Python per-frame script in MD Movie:<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

You would have to open the reference structure separately.  The per-frame Python script would:

(1) superimpose the reference structure (which could remain invisible) upon the current frame structure and show sequence alignment with both structures associated and RMSD header calculated, e.g. by running Chimera command “mm #0 #1 show true” if the reference structure were #1 and the trajectory #0 (because you don’t want to reposition the trajectory).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment>

Here’s a bit more on running Chimera commands via Python:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

(2) color to show values of the resulting residue attribute, e.g. Chimera command “rangecolor mavRMSDca,r min blue mid yellow max red”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

(3) close sequence alignment (this is why you would have to use a Python script, there’s no Chimera command for it… you’d also have to use Python if you wanted to specify calculating RMSDfull or RMSDbackbone instead of RMSDca).

This is a bit clunky and likely slow, so you may wish to weigh the pros and cons of using another program!  The automatic RMSD attribute assignment in Chimera is nice, however.
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 4, 2014, at 1:26 PM, Joshua Carter <carter_jjc at hotmail.com> wrote:

> Hey Elaine,
> 
> My apologies, I don't think I was clear enough about what I am trying to do.  I am interested in visualizing the movements of residues in a MDFF simulation via color in a single frame.  Essentially I want to capture the distance between each residue at the end frame of the simulation and at the beginning frame, and store those deltas as B-factors or other user defined attributes/variables that I can then use rangecolor on to visualize the results of a run in a single frame.  I was wondering if there was a way to do this using built in tools in chimera or if it was going to require some scripting in VMD.
> 
> Essentially I would like to do what you talked about in (A) but for each individual residue and be able to write it somewhere or store it in the pdb and then color the protein by it.
> 
> Thanks for any help and advice,
> 
> Josh
> 
> > Subject: Re: [Chimera-users] Visualizing MDFF Runs in Chimera
> > From: meng at cgl.ucsf.edu
> > Date: Fri, 31 Oct 2014 11:05:14 -0700
> > CC: chimera-users at cgl.ucsf.edu
> > To: carter_jjc at hotmail.com
> > 
> > Hi Joshua,
> > I don’t think this is something you can calculate with Attribute Calculator. That tool just does math on existing attributes rather than actually calculating RMSDs, which can be done in various other ways in Chimera. 
> > 
> > (A) If you mean overall RMSD (one value per frame) vs. a reference frame:
> > 
> > See MD Movie (the trajectory playback tool) menu: Analysis… Plot for calculating and plotting various quantities vs. trajectory frame number, including RMSD of specified atoms relative to a reference frame. There is a Dump Values button at the bottom to write out the values.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>
> > 
> > Unfortunately I’m somewhat at a loss as to what you would do next. My understanding is that Chimera doesn’t store separate attributes for different frames in a trajectory, so it wouldn’t be that simple. In a per-frame script in MD Movie, maybe you could use “setattr” to assign the value as an attribute and then “rangecolor” to map it to color, thus avoiding calculating the colormapping yourself. However, it is still ugly in that you have to get the right value assigned to the right frame.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> > 
> > (B) If you mean per-residue structural variability (one RMSD value per residue but considering all frames at once):
> > 
> > (However, I somewhat doubt this is what you meant, since it generally wouldn’t be shown during playback, but instead with coloring or worms on a single structure.)
> > 
> > This would be done by opening the whole ensemble at once (saving trajectory frames as a single multi-model PDB and then opening that the regular way instead of as a trajectory), superimposing the structures if they weren’t already, associating all of them with a single sequence, showing the sequence RMSD header, and then using Render by Attribute to show the per-residue RMSD values as coloring or worms on a single structure. More details on that approach in these previous posts:
> > 
> > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-September/010299.html>
> > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009710.html>
> > 
> > Sorry I couldn’t give a more definitive answer. Maybe this will get you closer, or others will have better ideas.
> > Best,
> > 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 Oct 31, 2014, at 8:00 AM, Joshua Carter <carter_jjc at hotmail.com> wrote:
> > 
> > > Hello,
> > > I am currently working on some MDFF simulations and have been visualizing them in chimera. I am trying to color the proteins by rmsd over the course of the simulation. I was thinking that there may be a way to do this using the attribute calculator tool between the first and last frames of the simulation. Does anyone know if this is possible or if there is a better way to do it?
> > > Josh
> > 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users