Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK
Hi Luca, After changing values, you need to click "Color" again. You can see the command appear in the Log each time that you click Color, containing the current values. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> If you mean you already did that but the coloring looks the same, it may be that most of your values are smaller magnitude than the values and it's just hard to see a difference. If you make the values much smaller (exactly to what depends on the data), the change may be more evident. I tested it just now to make sure, and the coloring is changing in my tests. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2021, at 3:36 AM, Luca Pellegrini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca
Dear Elaine, Thank you for your explanation. A couple of further questions, if you don’t mind: I can change the values in the Surface Color dialog box under Tools/Depiction, as you suggest. So how/when does one use the color key dialog box, which is a button within Surface color, to change red-blue values? Are there two ways to do this? How does Surface Color respond to changes in red-blue values? When I use the minimum, mean and maximum values for red, white and blue that appear in the log window after hitting ‘electrostatic’, the structure turns all blue. Apologies for being slow with this... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK
On 11 Oct 2021, at 17:10, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Luca, After changing values, you need to click "Color" again. You can see the command appear in the Log each time that you click Color, containing the current values.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>
If you mean you already did that but the coloring looks the same, it may be that most of your values are smaller magnitude than the values and it's just hard to see a difference. If you make the values much smaller (exactly to what depends on the data), the change may be more evident.
I tested it just now to make sure, and the coloring is changing in my tests. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2021, at 3:36 AM, Luca Pellegrini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca
Dear Elaine, Please ignore my message below, I figured it out (hopefully next time before hitting the send button). I have provided answers below, in the unlikely event someone else is as slow as me. Best wishes, Luca
I can change the values in the Surface Color dialog box under Tools/Depiction, as you suggest. So how/when does one use the color key dialog box, which is a button within Surface color, to change red-blue values? Are there two ways to do this?
The color key shows the boundary values as a colored bar (unrelated to surface coloring).
How does Surface Color respond to changes in red-blue values? When I use the minimum, mean and maximum values for red, white and blue that appear in the log window after hitting ‘electrostatic’, the structure turns all blue.
For this to work in Surface Color, one needs an electrostatic map (i.e. from apbs).
Best wishes, Luca
Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK
On 11 Oct 2021, at 17:10, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Luca, After changing values, you need to click "Color" again. You can see the command appear in the Log each time that you click Color, containing the current values.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>
If you mean you already did that but the coloring looks the same, it may be that most of your values are smaller magnitude than the values and it's just hard to see a difference. If you make the values much smaller (exactly to what depends on the data), the change may be more evident.
I tested it just now to make sure, and the coloring is changing in my tests. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2021, at 3:36 AM, Luca Pellegrini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca
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