[Chimera-users] same volume data values over the entire volume

Tom Goddard goddard at sonic.net
Mon Jul 22 12:16:08 PDT 2019

The message "no volume data for surface" doesn't make sense and I don't see that error message anywhere in the code.  But I do see the error message "No data values for surface" in the code.  If that is what you get it means that your surface is not within the bounds of the volume data.


> On Jul 21, 2019, at 11:22 AM, Blaas Dieter wrote:
> Hi Elaine,
> thank you very much, but with a slice again colouring only works with "volume data gradient norm" see attached image. When changing to "volume data" I receive the message "no volume data for surface" and pushing "colour" does not change the appearance. Is there anything wrong with my mrc file?
> bw Dieter
> On 2019-07-21 18:15, Elaine Meng wrote:
>> Hi Dieter,
>> I don’t know specifically what’s happening in your case, but if you
>> are coloring an isosurface of the same volume data, by definition all
>> the values would be essentially the same.  Coloring by the volume data
>> value would normally be used on a slice of that isosurface, e.g. as
>> shown here:
>> <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorcap <http://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#colorcap>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Jul 21, 2019, at 5:36 AM, Dieter Blaas <dieter.blaas at meduniwien.ac.at <mailto:dieter.blaas at meduniwien.ac.at>> wrote:
>>> Hi,
>>>    Trying to color a volume according to "volume data" I get the same numerical values for all colors and a speckled appearance. When using "volume data gradient norm" I get the expected colors, i.e. strong local changes of the volume data are red and spots where there is essentially no change are in blue. How is this possible? If I understand correctly, "volume data gradient norm" colors according to the first derivative of "volume data" or is this wrong?  Do I need something like a normalization?
>>> Thanks a lot for explanations,
>>> best, 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<image.png>_______________________________________________
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