[Chimera-users] translation matrix

Antón Vila Sanjurjo antonvila.s at gmail.com
Mon Dec 2 08:45:13 PST 2013

Hi Elaine,

thanks for your reply. I'm not interested in of superimposing structures
per se, Matchmaker does this beautifully, however it does not provide me
with the translation matrix used for the superposition. Since ribosome pdb
files are split in subunits, due to their large size, after I superpose one
of the subunits, I would like to have the translation matrix to superpose
the other. Does this make sense? I could get this information from other
pieces of software, of course, but I was wondering whether chimera could do
it as well.



On Mon, Dec 2, 2013 at 5:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Antón,
> You would first need to superimpose the two structures yourself.  I.e.
> "measure rotation" simply measures the transformation of one structure
> relative to another, after you have done something that moves it.  That
> command does not figure out how they should be moved.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation
> >
> Maybe superimposing the structures was your goal in the first place.  Ways
> to superimpose structures in Chimera are listed here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> Of the methods mentioned in the above, you might want to use Matchmaker
> but instead of defaults (trying all chains against all chains, which would
> take a REALLY long time for ribosomal subunits), choosing the option to
> specify exactly which chain(s) to use.
> 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
> On Dec 2, 2013, at 7:37 AM, Antón Vila Sanjurjo <antonvila.s at gmail.com>
> wrote:
> > Hi,
> > I'm trying to get a translation matrix for two different crystal
> structures of ribisomal subunits. I've been trying to use the "measure
> rotation" command but I can only get it to display the following message
> "rotation angle is near zero (0 degrees)". I was wondering whether the
> command might be failing due to the fact that the ribosome contains
> numerous chains, or perhaps because the command does not deal with RNA. At
> any rate, how would one go about obtaining a translation matrix that can be
> applied to any model?
> > best,
> > Antón
> >

Antón Vila-Sanjurjo, PhD
Marie Curie fellow
Grupo QOSBIOS, Dept. Química Fundamental
Facultade de Ciencias
Universidade de A Coruña (UDC)
Campus Zapateira, s/n
15.071 - A Coruña - España (Spain).

tlf: (34) 981-167000 ext:2659
e-mail: antonvila.s at gmail.com
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