[Chimera-users] Got it

Brian Cannon bcann001 at umaryland.edu
Thu Feb 24 11:22:31 PST 2011


Last night I learned that when you ctrl-click outside of the "Shown"
column of the dialog box, it works.  I'd only been clicking inside that

So, problem solved.  Thanks you very much for your help!


> 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.
> Elaine
> 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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