same volume data values over the entire volume
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 ------------------------------------------------------------------------ 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@meduniwien.ac.at ------------------------------------------------------------------------
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> 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@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
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>
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@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
On Jul 21, 2019, at 11:22 AM, Blaas Dieter <dieter.blaas@meduniwien.ac.at> 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?
Hi Dieter, How would I know??! The error message sounds like you did not specify a “volume file" in the Surface Color dialog, but since you colored by gradient, you must know how to do that. If I just open emdbID:5020 and slice it with Side View and then color its own surface by "volume data value" it looks as expected, image attached. You could try the same process with publicly available datasets and if only your data has the problem, you would suspect something is wrong with it. Only other idea is to make sure the values associated with the colors in Surface Color are reasonable, based on the range of values in the map as shown in the histogram in Volume Viewer. If you keep having a problem, instead of this guessing game, you should use menu: Help… Report a Bug and attach your data file and describe exactly the steps to reproduce your problem. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
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. Tom
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#c... <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@meduniwien.ac.at <mailto:dieter.blaas@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>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (4)
-
Blaas Dieter -
Dieter Blaas
-
Elaine Meng -
Tom Goddard