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

Tom Goddard goddard at sonic.net
Mon Jun 18 10:48:51 PDT 2018

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.


> On Jun 15, 2018, at 10:23 PM, Blaas Dieter <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> 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
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