[Chimera-users] color a small molecule in a .mol2 file by red to blue gradient of the partial charges

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 30 10:10:19 PDT 2013


P.S. If your mol2 file didn't already have charges, you can add them in Chimera (menu: Tools... Structure Editing... Add Charge, or command: addcharge).  It may call another tool to add hydrogens first if your structure doesn't already have them.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>


On Oct 30, 2013, at 10:03 AM, Elaine Meng wrote:

> Hi Francois,
> Yes, you can color by values of attributes such as charge with either the Render by Attribute tool (in menu under Tools... Depiction) or with the command "rangecolor".  When you read in a mol2 file with charge values the "charge" attribute is automatically assigned.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> 
> There are several examples of using these in the tutorials.  The attributes tutorial part 1 uses both:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part1>
> 
> The rangecolor example in that tutorial specifies particular values for red and blue, but as the man page says, you can also use the words "min" and "max" to mean the minimum and maximum charge values present in your molecule, e.g.:
> 
> rangecolor charge min red 0 white max blue
> 
> The GUI (Render by Attribute tool) has the advantage of showing you the range in a histogram and also displaying the names of the various attributes, although in this case it's just "charge".  There are more examples of coloring by attribute in the attributes tutorial part 2 and the surface properties tutorial.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
> 
> There are several ways to switch to white background, including any of the publication presets and command "background solid white":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html>
> 
> The image tips page covers many image-related topics such as background color. You can just click the "Tips" button on the image-saving dialog to show it.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
> 
> 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 Oct 30, 2013, at 12:29 AM, Francois Berenger wrote:
> 
>> Is it possible to do this in Chimera?
>> 
>> I'd like a white background too.
>> 
>> Thanks a lot,
>> F.
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> 
> 
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