[Chimera-users] user-defined attributes

[Elaine Meng]

Hi Lisa,
After you define the attribute, the "Render by Attribute" dialog appears so you can apply the coloring.  I assume that is what you already used.  This dialog has a histogram of the values, and the vertical bars on the histogram define a mapping between colors and values.  You can drag the bars on the histogram and change their colors individually to define the mapping however you want, and/or you can choose a different color "Palette" to change their colors all at once.

If you did the coloring and clicked OK, that dialog was dismissed, but you can reopen it by choosing "Tools... Depiction... Render by Attribute" from the menu.  If you click Apply instead of OK, that will apply the coloring without dismissing the dialog.

How to use Render by Attribute:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
...and specifically its coloring section:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#colors>

However, I will be in the office N476B Genentech Hall tomorrow Thurs Jan 6, for the most part -- if there is a time you would like to stop by, say within the 9-5ish range, let me know (just email me off-list) so I will know when to stay put. 
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Jan 5, 2011, at 3:20 PM, Watson, Lisa wrote:

> Hi Elaine,
> I am trying to create some figures using Chimera.  I used "define attributes" to color my protein structure according to values from data I generated.  Now I would like to manipulate the heatmap color scheme as well as to manipulate the threshold for the various colors.  Could you give me some tips on how to do this, or better yet, is there a time I can stop by your office to learn how to do this?
> Thanks,
> Lisa