[Chimera-users] hold the clipping of EM density map

[Elaine Meng]

Hi Jianhao,
The Side View only clips the viewing area.  As you saw, it does not crop the map, just hides the front and/or back parts that are outside the Side View planes when you rotate it. 

There are two general choices…

(A) if this is just for display and you don’t need to actually crop the data, you could use “per-model clipping” which is a clipping plane or slab that moves along with the model (in this case your map).  There is a Per-Model Clipping GUI (in Tools menu under Depiction) that allows you to interactively adjust the clipping plane location with the mouse:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>

(there is also a command, but it’s harder to position the plane with the command)

Discussion of global vs. per-model clipping planes:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>

(B) you could actually crop the map, e.g. smaller rectangular box by entering different region bounds (show with Volume Viewer menu: Features… Region Bounds) or draw a box with the mouse to crop as described in this previous post.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-April/014510.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 17, 2018, at 5:30 AM, C.J. <biocjh at gmail.com> wrote:
> 
> Hi specialists,
> I tried to clip half part of a EM density map using "Tools->Viewing->Side View". 
> And then, I tried to rotate the map with specified part of the map clipped. But I failed to.
> Only the part toward me was clipped.
> Am I missing something?
> Regards,
> Jianhao