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

[George Tzotzos]

Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference.

I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I’d like to render these ranges of residues semitransparent. I’ve tried to do this with the transparency command but this applies to ribbons only (I think). 

I’d appreciate any suggestions as to how this can be done.  

Thank you in advance

George


From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: coloring by RMSD (conformational variability)
Date: 25 March 2014 at 19:32:47 GMT+1
To: George Tzotzos <gtzotzos at me.com>
Cc: chimera List <chimera-users at cgl.ucsf.edu>
Reply-To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>

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
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