[Chimera-users] Visualizing MDFF Runs in Chimera

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 5 11:32:59 PST 2014

Hi Josh,
	If all you want to do is show the variance between the first frame and the last frame, ignoring intermediate frames then that's easy.  Save the first and last frames as PDB files.  Open the first frame and show its sequence.  Open the last frame and superimpose it on the first frame (e.g. the command "mm #0 #1") and then use the sequence dialog's Structure->Associations menu item to also associate the last frame with the first frame's sequence.  Then use the dialog's Headers->RMSD:ca menu item (or whichever RMSD header you prefer) to show the per-residue RMSD on the sequence.  This will also create a 'mavRMSDca' attribute in each residue that you can the use the Render By Attribute tool (or rangecolor command) to color your structures with.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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
> > 
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