[Chimera-users] coloring by RMSD (conformational variability)

George Tzotzos gtzotzos at me.com
Tue Mar 25 17:05:24 PDT 2014

Hi Elaine,

Your help as always is invaluable. I have not tried your suggested routine but I’m sure it works. 

The reason for this is that I was trying to find out why all residues are shown as ALA. In analyzing the  Principal Components of my Amber trajectory, I used for first time an R-based program (Bio3D). I followed a tutorial using my own data rather than those of the tutorial (http://thegrantlab.org/bio3d/tutorials/trajectory-analysis). According to this tutorial, only the C-a atoms are selected for superposition. 

Thanks once again for your kind help


On Mar 25, 2014, at 3:32 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi George,
> Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color.  The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work:
> (1) show the sequence (menu: Favorites… Sequence).  Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence.
> (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure… Associations. In that dialog, change all the "none" to the same sequence, then click OK.  This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence.
> (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers… RMSD.  Now the sequence window will have an RMSD histogram above the sequence.  It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low.
> (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools… Depiction).  In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence).  It will show a histogram of the values with some vertical colored bars.  You use those bars to define how the values are mapped to color.  The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click.  You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that.  You can keep clicking Apply and then adjusting the coloring until it is how you like it.  For example, I show coloring by RMSD from blue->red->yellow  (and then menu: Presets… Publication 1) in the attached image.
> 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
> <rmsdcolor.png>
> On Mar 25, 2014, at 10:03 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> Hi everybody,
>> I’ve conducted Principal Component Analysis on a trajectory and generated an ensemble of structures (see attachment, pc2.pdb). There should be a way of coloring (occupancy?) the most mobile regions of the protein (e.g. residues 67 - 72). 
>> I haven’t found a way to do this. Any help would be much appreciated.
>> Best regards
>> George
>> <pc2.pdb>

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