[Chimera-users] structural alignment

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 7 09:44:17 PDT 2010

Hi Bala,
The recommended single-sequence procedure now works (daily builds dated Jul 7 2010 or later), and it's no longer necessary to resize the window manually before showing the RMSD header.

On Jul 6, 2010, at 3:26 PM, Elaine Meng wrote:

> You would just show the sequence of one copy, then associate all the structures with that sequence, then show the RMSD header.  The RMSD header bar heights represent the RMSD among residues at each position, and it is also available as the residue attribute mavRMSD for display with colors and "worms" using Render by Attribute.
> (1) showing sequence.  Choose Favorites... Sequence, pick any one of the RNA chains.  Remember which one you chose.
> (2) associating.  In the sequence window menu, choose Structures... Associations and set all of the other structure models to also associate with that same sequence, OK.  This could also be done if the sequences were not identical but highly similar.
> (3) superimposing.  In the sequence window menu, choose Structure... Match and superimpose everything.  Don't turn on any of the options, just click OK.
> (4) showing RMSD header.  In the sequence window menu, FIRST make the sequence area larger vertically by resizing the window (necessary to avoid a technical problem) and then choose Headers... RMSD.
> (5) showing RMSD values on a structure with color and/or "worms."  You would probably hide all the structures except one (e.g. command: ~modeldisp #.2-end), then choose Tools... Depiction... Render by Attribute, and in that dialog, use the attribute of "residues" named "mavRMSD" of the same model as you are displaying, etc.  You can adjust the mapping of values to color or worm radius however you like, as explained here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

(alternatively, save sequence window as EPS image and/or save mavRMSD values to file)

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