[Chimera-users] Saving Attribute settings and Worm Radius Consistency

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 26 11:54:55 PDT 2016

> On Jul 25, 2016, at 2:24 PM, Nicole Persky <persky at broadinstitute.org> wrote:
> Hi All,
> I've started using Chimera to map two different datasets onto structures. 
> For one, we use color, and for the other we use worm radius.
> I've encountered two problems while trying to make figures for publications:
> 1- when I save my session the image is saved but when I go to "render by attribute" to tweak the settings a little, the threshholds under colors and worm radius have been reset. 
> How to I get them not to reset, but to keep the thresholds?

Hi Nicole,
	Render By Attribute doesn’t put any information into session files.  Even if it did, it would only “half help” here, because the tool forgets your settings for one attribute as soon as you switch to the other, so it would only be remembering one attribute’s settings at most.  There is a quasi-awkward workaround.  Once you get the settings for an attribute the way you want, save a scene.  Render By Attribute will preserve the current attribute settings in the scene.  One quick way to save a scene is to use the lightning bolt button on the lower right of the Chimera window to show the Rapid Access screen, then choose the “Save scene...” button in that, then click the “+” button in the resulting Scene dialog.  You would want to save one scene per attribute.  You can rename the scene to something more mnemonic by right-clicking on the scene in the Scene dialog and choosing “Properties” in the popup menu to edit the scene name.  Scenes are saved in sessions.

> 2- I am trying to compare three different images with the same worm radius thresholds. 
> For one of the images the lowest number of my attribute is LARGER than the lowest number I want to define on my threshhold (I would like to set the lower worm radius to 1 for a value of 1 however for this dataset my lowest value is 2. I cannot just set the value starting at 2 because there is a gradient to the largest value that gets thrown off). Yet, I cannot set the threshold lower than the lowest value of my attribute. Does anyone know a way around this?

You can’t drag the bars off the edge of histogram, but in the “Value” entry field for the current bar you can type in numbers that are beyond the bounds of the histogram.  The histogram will then expand to show the larger range.


	Eric Pettersen
	UCSF Computer Graphics Lab

> thanks so much,
> Sincerely,
> Nicky
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