[Chimera-users] structural alignment

Bala subramanian bala.biophysics at gmail.com
Tue Jul 6 15:59:37 PDT 2010

Dear Elaine,
Thank you. But i have a problem in doing this because my RNA has two
principal chains [two strands seperated by TER card, attached pdb file]. It
would be nice if there is a way to output the rmsd so that i can make a box
plot to show which residues are flexible among those conformations.

Thank you,
On Wed, Jul 7, 2010 at 12:26 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bala,
> Since they are the same sequence, you don't need a sequence alignment, but
> we had to make a small fix in Chimera to allow it, so you would need the
> *next* daily build to follow this recipe.  (or skip down to the lower part
> of this message for a different approach you can do now!)  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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers
> >
> (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
> >
> Actually, Eric just told me that you can do a similar thing now (without
> the fix I mentioned) by making a sequence alignment instead of taking the
> more elegant single-sequence approach.  Here is that alternative recipe:
> After #1 above,
> (2) add one more copy of the sequence to make an alignment of two
> sequences.  FIRST make the sequence area larger vertically by resizing the
> window (necessary to avoid a technical problem). From the sequence window
> menu, choose Edit... Add Sequence, choose From Structure, and choose any
> copy of the chain that is *different* than the one you chose in #1.  In your
> case (RNA) you also need to change the Matrix to "Nucleic" before clicking
> OK.  Now you should have an alignment of two sequences with all the other
> structures automatically already associated with the second sequence.
> Then carry on with #3-5 as above.
> Below I attach an image showing RMSD with colors blue->red->yellow and
> worms for an NMR ensemble of RNA, NDB entry 17ra.  Only the first member of
> the ensemble is shown.
> 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
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