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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Mon Jun 18 15:26:18 PDT 2018

Dear Tom,

     thank you very much for these explanations. I shall try in the next 
days and report!

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 18.06.2018 um 19:48 schrieb Tom Goddard:
> Hi Dieter,
>   This cannot be done easily.  To do it you would want a a gradient 
> norm map, then you could mask your map setting all the values to zero 
> where the gradient norm is small. The surface color tool you are using 
> does not compute a gradient norm map — it just computes gradient norm 
> values on the surface which is not good enough for your use.  Even if 
> you get the gradient norm map, I see lots of red in the blue region so 
> masking is going zero many grid points in the interior of the virus. 
>  You could try to smooth (Gaussian filter) the gradient norm map to 
> avoid that.  Finally it is possible to get the gradient norm (squared) 
> by just using "vop subtract”, “vop multiply” and “vop add”.  There are 
> a lot of steps to it — basically you do a center difference along each 
> axis, in other words take 2 copies of the map shift one by 1 voxel 
> along -x and the other by 1 voxel in the +x direction, then subtract 
> them.  Do the same along y and z axes.  The 3 resulting maps give you 
> the 3 components of the gradient vector.  Square each component (vop 
> multiply map times itself), then sum the 3 squared components and you 
> have the norm squared.  There is no square-root operator so hopefully 
> the norm squared would suffice.
> Tom
>> On Jun 15, 2018, at 10:23 PM, Blaas Dieter 
>> <dieter.blaas at meduniwien.ac.at 
>> <mailto:dieter.blaas at meduniwien.ac.at>> wrote:
>> 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 
>>>> <mailto: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 
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