[Chimera-users] Density map tranformation

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 22 12:58:56 PST 2020

The match command reports the transformation of one model compared to itself before running that command, whereas measure rotation would report any current transformation of one model relative to another model.  If you expect those to be the same, but the difference is small, it might just be rounding differences.


> On Dec 22, 2020, at 12:31 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Thanks a lot. I had experimented with fitting pdb structures and calculating their transformation with the match move false showMatrix true command, which slightly differ than measure rotation, I wonder why. 
> On Mon, Dec 21, 2020, 9:13 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> You can report in the Reply Log the transformation of a model relative to another model with "measure rotation"
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
> Also, you can save the current overall transformation of models (including any rotations/translations of the whole scene) to a text file with command "matrixget"
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Dec 18, 2020, at 10:09 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> > 
> > Hello,
> > 
> > When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that?
> > 
> > Best regards. 

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