[Chimera-users] extract parts of a map based on 'volume data gradient norm'

[Dieter Blaas]

Dear Elaine,

    thank you! I am sorry, but I do not understand: how do I get the 
isosurface? What is the command? Carefully adjusting the boundaries of 
the gradient norm, I got a blue and a red part. How can I make an 
isosurface of one of them? Is this a function in the GUI or do I have to 
use the command line? Can you please give an example of how to proceed!

Thank you very much, bw Dieter

------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: dieter.blaas at meduniwien.ac.at
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Am 15.06.2018 um 18:56 schrieb Elaine Meng:
> Hi Dieter,
> If I understand correctly, you have two maps, the original volume (density) and then another with gradient norm that is used to color the first.
>
> In that case, you could show an isosurface of the gradient norm values, then use the “mask” command to mask the original density map by the gradient-norm isosurface (i.e. zero out parts inside or outside the isosurface):
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.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 Jun 14, 2018, at 10:43 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
>>
>> Hi,
>>        I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume!
>>
>> Thanks for hints, bw, Dieter