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

Blaas Dieter dieter.blaas at meduniwien.ac.at
Fri Jun 15 22:23:20 PDT 2018

Dear Elaine,
    thanks a lot! Here it is! I open a volume, colour it according to 
'gradient norm' and would like to save the red or the blue part of the 
whole (not just the half of the virus shown!
bw Dieter

On 2018-06-16 00:06, Elaine Meng wrote:
> Dear Dieter,
> An isosurface is just the surface of a density map showing a certain
> level, i.e. the “surface” display in Volume Viewer.
> Do you have one map or two maps?  I tried to ask that by saying “if I
> understand correctly” in my previous message.  I thought you were just
> coloring the isosurface of one density map by the values in a second
> map, where the second map is gradient norm map.
> It might help if you attached a picture of the display and Volume
> Viewer dialog.  “blue part” and “red part” are ambiguous.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jun 15, 2018, at 2:51 PM, Dieter Blaas 
>> <dieter.blaas at meduniwien.ac.at> wrote:
>> 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

Dr. Dieter Blaas
Max F. Perutz Laboratories,
Inst. Med. Biochem.,
Med. Univ. Vienna
Dr. Bohr Gasse 9/3
A-1030 Vienna, Austria
Tel. 0043 1 4277 61630
Fax  0043 1 4277 9616
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