[Chimera-users] Group cylinder with a PDB and fit together

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 7 08:37:56 PST 2013


Hi Mario,
One way is to apply the transform of the PDB to the cylinders, after the PDB has been fit.  Example command if the PDB is model 0 and the cylinders are model 1:

matrixcopy 0 1

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html>

I believe yes, you would have to open the BILD file multiple times to get multiple sets of the cylinders it describes.

There are other ways to create cylinders that don't require you to create and open a separate file:

(A) command "shape cylinder" … arbitrary coordinates that you specify, similar to the BILD approach
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#cylinder>

(B) command "define axis" for best-fit axes to groups of atoms … unlike the above, these will move along with the atoms automatically.  Length and orientation are calculated from the specified atoms, you cannot specify them arbitrarily.  This is also implemented in the graphical interface "Axes/Planes/Centroids"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

Other advantages of these other two approaches is that you can change their color after the fact, unlike the BILD cylinders.

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 Nov 7, 2013, at 7:08 AM, Mario Dejung <chimera.maillist at dejung.net> wrote:

> Hi all,
> I created a some cylinders in chimera to visualise the symmetry axis and the rotation center of a hexametric structure. Is there a way to fix the position of these cylinders relative to the pdb structure? So when I fit the structure, the cylinders will also rotate in the same way.
> 
> And, by the way, is it possible to duplicate these cylinders, or do I have to create a .bild file and import it several times?
> 
> Thanks for your feedback.
> Mario




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