[Chimera-users] rotate a helix

Elaine Meng meng at cgl.ucsf.edu
Fri May 23 11:59:52 PDT 2008

Hi Maurice,
Firstly, I would only recommend this type of work for generating a  
crude model, such as for a figure.  I doubt that the quality would be  
high enough for work that depends on the detailed atomic  
coordinates.  Energy minimization can only "rescue" local strains and  
conflicts, so if you start with something ridiculous you will still  
have something ridiculous after minimization!  For a higher-quality  
model you would need to do more complicated conformational sampling  
and energy evaluation, either by creating it with some other program  
that includes such calculations, or by performing such calculations  
with another program after building the initial model in Chimera.

Given those caveats, however, here are some ideas:

(A) use Movement Mouse Mode (under Tools... Movement) set to "Move  
helix, strand, or turn" - this lets you move interactively whichever  
unit of secondary structure you "grab" with the mouse.  You do not  
have to break any bonds, they will just distort.  You can still move  
the entire structure when the cursor is in the window but not on top  
of any atoms.  The drawback here is that instead of entering a  
specific angle you would have to approximate the amount of movement  
interactively.  Before moving the helix, specify the center of  
rotation, for example by selecting one or more atoms and choosing  
Actions... Set Pivot or using the command cofr and specifying those  
atoms.  The Movement Mouse Mode tool includes an "Undo Move" button  
so you can recover from mistakes.  Save a PDB file of the result.

If you have a recent version of Chimera, you can measure the crossing  
angle of the original and modeled helices using the Axes tool (under  
Tools... Structure Analysis).

(B) if you really want to rotate the helix exactly X degrees, the  
only way I know of is to put that helix in a separate file.  You  
could open the original file with the whole structure for comparison,  
and then a second file with just the helix.  Move the structures in  
tandem to get a position where the rotation you want is around the  
screen axis X (horizontal in plane of screen), Y (vertical in plane  
of screen), or Z (normal to screen).  Then freeze the original  
structure (for example by unchecking its Active box in the Model  
Panel, which is under Favorites), specify the center of rotation as  
in (A), and then use a command to rotate the helix:
   turn y 45
(or x or z depending on how you set up the view).  Then save the PDB  
file of the helix "relative to" the original structure.  To merge the  
helix back in, you would have to text-edit the whole structure file  
to replace the old coordinates with the new coordinates.

After (A) or (B) and making sure you have saved those results to a  
file, you can consider whether or not minimization will improve the  
structure.  I am skeptical that it would help very much.  You would  
probably want to freeze some parts of the structure and do it in  
different stages freezing different sets of atoms to lessen  
distortions and keep the helix approximately in the intended  

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 22, 2008, at 10:03 PM, Maurice Ho wrote:

> Hi there,
> I would like to rotate a helix at a particular angle.  How could I  
> accomplish the following?
> 1. How to define the central axis of the helix in chimera?
> 2. How to set a particular angle to rotate?
> 3. I do this on a helix belonging to a GPCR, with the loops firstly  
> broken for rotation and then perhaps need to rejoin them.  How to  
> join them back?
> 4. After joining, should I just redo energy minimization for the  
> loops concerned?
> Much thanks!

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