[Chimera-users] rotate a helix
meng at cgl.ucsf.edu
Fri May 23 11:59:52 PDT 2008
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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