Change default pseudobond color?
Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli
Hi Oli, There is no default color for pseudobonds in general, but I guess you mean distance monitors? In that case, you can open the Distances tool (in menu under Tools... Structure Analysis), change the color, and then click the button to "Save" as defaults for subsequent uses of Chimera. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances> Most effort is on ChimeraX these days: We did change the factory default colors in ChimeraX for pseudobonds showing hbonds, contacts, and clashes specifically for this reason, so that they show up on both black and white backgrounds (and there is also a keyword to specify any color). For distances, ChimeraX has a Distances preference category to set the default color etc. however you like. <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#distances> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 10, 2020, at 12:01 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli
That is exactly what I was looking for, thanks Elaine and apologies for the spam! I was looking under the pseudobond panel, where I usually change the color, and couldn’t find a way to save as default. Many thanks! Cheers Oli
On Mar 10, 2020, at 3:30 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There is no default color for pseudobonds in general, but I guess you mean distance monitors? In that case, you can open the Distances tool (in menu under Tools... Structure Analysis), change the color, and then click the button to "Save" as defaults for subsequent uses of Chimera. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
Most effort is on ChimeraX these days: We did change the factory default colors in ChimeraX for pseudobonds showing hbonds, contacts, and clashes specifically for this reason, so that they show up on both black and white backgrounds (and there is also a keyword to specify any color). For distances, ChimeraX has a Distances preference category to set the default color etc. however you like. <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#distances>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 10, 2020, at 12:01 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli
participants (2)
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Elaine Meng -
Oliver Clarke