[Chimera-users] chimera utility help

[Eric Pettersen]

On Sep 13, 2012, at 9:17 AM, Elaine Meng wrote:

> A second possibility is to rotate each phi and psi angle in your current structure, using either Build Structure, Adjust Torsions section, or the "rotation" command.  However, I think that would be difficult, or at least quite tedious and labor-intensive.

Along these same lines, since phi/psi angles are residue attributes, you can use the setattr command to set them.  For instance, an alpha helix has phi/psi angles of -57/-47.  So your original extended structure that looked like this:



Could at least be changed into a couple of alpha helical segments like so:



Your extended structure has a lot of prolines in it, which means it cannot easily be made into one helix since prolines cannot have their phi angles changed without corresponding adjustments to the side chain ring (which is why prolines are known as "helix breaking" residues), so maybe the other approaches that Elaine suggested are better here.

--Eric

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120913/878d9f8f/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 16390 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120913/878d9f8f/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen shot 2012-09-13 at 11.09.14 AM.png
Type: image/png
Size: 173424 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120913/878d9f8f/attachment-0001.png>