[Chimera-users] question on visualization

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 1 09:26:35 PST 2017


There’s also a “volume” command “capFaces” option, e.g.

volume #3 capFaces false

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dispsurf>

Elaine

> On Dec 1, 2017, at 2:10 AM, C.J. <biocjh at gmail.com> wrote:
> 
> Thank you very much!
> regards,
> Jianhao
> 
> 2017-12-01 17:28 GMT+08:00 Gabor PAPAI <papai at igbmc.fr>:
> Hi Jianhao,
> You have to untick the “cap high values at box faces” to see surfaces bellow 0 threshold. You can find this option in Volume Viewer -> Features -> Surface and Mesh options at the bottom of the panel.
> Best regards,
> Gabor
> ---
> Gabor Papai
> IGBMC
> Integrated Structural Biology
> 1, rue Laurent Fries, Bp 10142
> 67404 Illkirch, France
> Tel: +33-3-69485288
> 
>> On 1 Dec 2017, at 4:43 , C.J. <biocjh at gmail.com> wrote:
>> 
>> Hi specialists,
>> I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? 
>> Some snapshots of the visualization in both programs are attached to the post.
>> Thank you!
>> regards,
>> Jianhao




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