Hi Lisa, Yes, you could do exactly that same thing, and then what is shown as "bfactor" in the Render by Attribute dialog is really whatever values you put in the PDB file.

However, Chimera is even more flexible in that you can create your own custom attributes and assign their values with a different file, instead of having to edit the input PDB file. An "attribute definition" file is a simple text file, and it is less limiting because you can have several different custom attributes at the same time, with whatever names you have assigned them (not necessarily "bfactor"). An attribute definition file is read in using the Define Attribute tool or the command "defattr." A description of the format and links to several examples can be viewed here:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile

I hope this helps, 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 Aug 26, 2010, at 4:21 PM, Watson, Lisa wrote:

Hi Elaine, Is it possible to use the Render by Attribute function to color code a structure according to data values that can be entered for each residue? In pymol this can be done by replacing overwriting b values with other data. Thanks, Lisa

On Aug 27, 2010, at 8:53 AM, Forbes J. Burkowski wrote:

Hi:

At the risk of being a heretic, I would like to ask the following question:

Is it possible to use the Wingware Python IDE instead of IDLE to edit and execute Python scripts for Chimera?

More information about Wingware can be found at wingware.com.

I suppose that if Wingware is given the appropriate pathnames it could import chimera and other needed packages. So, it could be used as Python script editor. However, I am hoping that it could also be used to run and debug scripts that interact with the Chimera window. Would this be possible?

First off: heretic!

;-)

Second, the new face in our lab, Darren Weber, has developed a wiki page describing how to get the Eclipse IDE to work with Chimera:

http://plato.cgl.ucsf.edu/trac/chimera/wiki/ChimeraEclipse

Perhaps some of the information there could be adapted to getting Wingware to interface with Chimera.

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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