[Chimera-users] partial conservation coloring

Eric Pettersen pett at cgl.ucsf.edu
Tue Feb 28 11:55:08 PST 2012

Jill Voreis wrote:
> I'm trying to use chimera to show conservation maps. Using pdb files  
> that I fetch from the database using the pdb id number and  
> alignments created in clustal that contain the sequence of the pdb  
> file, I select render by conservation. For some reason, the  
> conservation colors only go onto  my model when it's in ribbon form.  
> When I try to show the surface representation or use spheres so that  
> I can use commans to show the SAS, the colors of my model do not  
> match the conservation model but rather are stuck on some sort of  
> coloring scheme related to the compounds that are there. The  
> majority of the map looks brown, like the default color before  
> rendering by conservation. If you could help me, I'd really  
> appreciate it!

Hi Jill,
	There are a few possibilities here, though it's impossible to be  
certain what the problem without access to a concrete example.  My  
best guess is that much of the surface region of your protein is  
poorly conserved and those areas have columns where the rows are more  
than 50% gap characters.  For such columns no conservation score is  
assigned.  That means that when you use Render By Attribute with  
default settings, those atoms / surface parts will retain their  
original colors.  If in Render By Attribute you use the "No-value  
color" color well to assign a color to such regions (perhaps gray) you  
will be able to tell if this is what is happening.
	Two other possibilities are that you don't have the "Color atom" and  
"Color surfaces" check boxes checked [though I image you would have  
noticed this!] or that your protein has multiple chains and that only  
one is associated with the alignment and only that one is getting  
	If none of these are "it", if you can provide me with a specific  
example so I can reproduce the behavior then I will investigate.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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