[Chimera-users] Fussy density around the particle

[Elaine Meng]

On Nov 14, 2012, at 4:04 AM, Mohit Kumar wrote:

> Hi Elaine,
> Can you please tell me how to remove the fussy density from the plane of a
> particle?
> I went to Volume Viewer>Features>Planes>One to make a plane of the particle.
> I can see a fussy density around the particle at the entire boundary.
> How can I deactivate it ??
> Thanks in advance.
> Best,
> Mohit
> 
Hi Mohit,
Please send chimera questions to chimera-users at cgl.ucsf.edu rather than to me directly -- it allows other people to answer if I cannot, and allows other users to benefit from the information.

In this case, I may not understand the question.  You could

(a) adjust the thresholds for density display using the Volume Viewer dialog
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsolid>

(b) filter your map using Volume Filter (in menu under Tools... Volume Data)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html>

(c) erase parts of a map using Volume Eraser
(d) segment using Segment Map
etc... see "volume tour"
<http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>

Best,
Elaine