[Chimera-users] Inter-helical angle?

Brian Cannon bcann001 at umaryland.edu
Wed Feb 23 13:40:47 PST 2011


Thank you for your response; I think I'm close to getting the information
that I want.

I need to calculate the angle between helices one and four of calmodulin. 
When I click on "Define axes" and select the "Each helix in" link, the
radius values get written to the dialog box.  I de-selected all helices,
and clicked on H1 and H4, but didn't see an angle value pop up on the
dialog box, as expected.  I did figure out how to save the "axis name,
length, center, direction" values into a separate file.

Am I missing something that will bring up the H1-H4 angle automatically,
or do I need to use the information in the separate report file (made by
clicking "save") to calculate it?  If so, can you point me to a formula?

I'm attaching the pdb file I'm working with and I'm using a Mac, if that
makes a difference.  Any additional information you could provide would be
greatly appreciated; I can also talk to someone via telephone, if
necessary.  Thanks again, and I hope to be citing your program in short


> Hi Brian,
> You can use the Axes/Planes/Centroids tool to define helix axes, then get
> the angles between them.  It can do much more -- as implied by the name,
> you can define axes, planes, or centroids for various groups of atoms and
> then perform measurements among any of those objects.
> - choose from menu: Tools... Structure Analysis... Axes/Planes/Centroids
> - on the dialog, click "Define axes" and you might as well just take the
> defaults to define axes for all helices in your structure
> - the axes will be listed in a table, and you can measure distances/angles
> between any pair by choosing them in the table (click on one, Ctrl-click
> on the second); that will report the crossing angle and distance at the
> bottom of the dialog and in the Chimera Reply Log
> For more information on the tool and its options, see the manual page by
> clicking the Help button on the dialog, or going here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
> You can also define axes and measure the angle with commands instead of
> the graphical interface:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> 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 Feb 22, 2011, at 11:23 AM, Brian Cannon wrote:
>> I need to calculate the angle between two helices in a protein.  Do you
>> have any instruction about how I could go about doing this?
>> Any help would be greatly appreciated.  Thanks!
>> Brian

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