Hi Hatuey, It may not be problem. You did not give very much information, but I am guessing you are using the ribbons preset and different proteins. If a protein just has one chain, that chain is rainbow-colored from blue at the N-terminus to red at the C-terminus. If there are multiple chains, each chain is instead its own color. Or, if you have more than one model, each model is instead its own color. It probably does not matter what programs were used to prepare the structure file. The preset tries to adapt to the situation to make it easy to see your structure(s) in a single step. For example, if you had 12 chains in 3 different models, it would be too confusing if each chain was rainbow-colored, but when you only have one, it helps you understand the structure. Of course, if you don't like how anything is shown, just change it. There are many different ways to change colors, display styles, what is displayed, etc. (using Select and Actions menus, commands, other Tools). The presets are just meant to be quick and convenient but of course cannot cover every possible way you might want to show the structures. We have beginner tutorials included with Chimera, see "getting started": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html and there is an expanded, more detailed "getting started" tutorial at our web site: http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 23, 2007, at 10:52 AM, Hatuey Hack wrote:

Hi all,

As a Chimera new users, I notice that the proteins are rendering different depending on the program they where prepared.

I used the preset to render them. I have a protein with all residues in different color and the other protein is rendered in a single color.

My question is: this is a problem of Chimera or it is a problem with the protein file?

Regards,

Hatuey _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users