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