[Chimera-users] Cross-section question

Tom Goddard goddard at sonic.net
Fri Oct 18 11:06:58 PDT 2013


Hi Lawrence,

  Sure it is easy to see plane 72.  Use the Volume Viewer dialog, show the planes panel (menu Features / Planes), press the "One" plane button in that panel and set the plane number entry field to 72.  To assure you see the full resolution data make sure "Step" is set to 1 above the volume dialog density map histogram, and that "depth" is set to 1 in the Planes panel.

  This and other Chimera density map features are described in the Chimera guide to volume data display

	http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html

  Tom



On Oct 18, 2013, at 10:09 AM, "Tartaglia,Lawrence J"  wrote:

> Hi Tom,
> 
> Thank you for getting back to me. I should have been a bit more clear. What I want is the exact "central" section. I'm not sure if you are familiar with cryo-electron microscopy? I used a box size of 143 pixels to box my virus particles. What I would like to see if image 72 (central section) of my reconstruction. Is there a way to do that? I've attached an image of an example central section (left hand side) using the program IMOD. I'm sorry for the confusion...
> 
> Best,
> 
> Lawrence
> 
> 
> On Thu, 17 Oct 2013 09:43:43 -0700, Tom Goddard wrote:
>> Hi Lawrence,
>> 
>>  I'm not sure what you mean by "exact cross-section".  Do you mean
>> aligned to the virus map grid axes?  If so the Orient button at the
>> bottom of the volume viewer dialog will do that.  But probably it is
>> better to simply specify which planes to show using the Region Bounds
>> panel of the volume viewer dialog (Features menu) - specify a z range
>> 120 125 1 to show planes 120 to 125 using step 1 (i.e. every plane).
>> This will be better than using clip planes.
>> 
>>  Tom
>> 
>> 
>> On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" wrote:
>> 
>>> Hello,
>>> 
>>> I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this?
>>> 
>>> Thanks!
>>> 
>>> Best,
>>> 
>>> Lawrence
>>> --
>>> Lawrence J. Tartaglia, Ph.D.
>>> Postdoctoral Scientist
>>> Agbandje-McKenna Lab
>>> Department of Biochemistry and Molecular Biology
>>> College of Medicine, University of Florida
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
> 
> -- 
> Lawrence J. Tartaglia, Ph.D.
> Postdoctoral Scientist
> Agbandje-McKenna Lab
> Department of Biochemistry and Molecular Biology
> College of Medicine, University of Florida<Screenshot-1.png>




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