[Chimera-users] Inter-helical angle?

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 23 19:06:55 PST 2011

Hi Brian,
To choose two rows in the dialog (two helix axes in this case), you need to click one and Ctrl-click the other, as mentioned previously.  It sounds like that may be where you went wrong, since there was no problem defining the helix axes for your protein.  The two chosen rows in the dialog will be highlighted and the relevant measurements reported near the bottom of the dialog and in the Chimera Reply Log. 

On Feb 23, 2011, at 1:40 PM, Brian Cannon wrote:

> Elaine,
> 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
> order!
> Brian
>> 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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