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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Fri Jun 15 14:51:57 PDT 2018

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

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

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