[Chimera-users] Hello~ how to make a 3D structure for a number of family genes

tao zhao zhaotaoshine at hotmail.com
Tue Dec 4 23:55:21 PST 2012

I can do it now.Thank you so much for your help! You really save me a lot of time. Thank you and Merry Christmas.
Best regards,Tao.

> Subject: Re: [Chimera-users] Hello~ how to make a 3D structure for a number of family genes
> From: meng at cgl.ucsf.edu
> Date: Tue, 4 Dec 2012 15:58:53 -0800
> CC: chimera-users at cgl.ucsf.edu
> To: zhaotaoshine at hotmail.com
> Hi Tao,
> If you wanted a 3D model of each different protein you would just repeat the Modeller process 35 times. 
> However, it sounds like maybe instead you want to color one structure to show sequence conservation in the family.  In that case you would need:
> (1) one 3D structure, which you already made (or maybe even just the template structure would work)
> (2) a sequence alignment containing the 35 sequences
> Although you can add sequences one by one to make a sequence alignment in Chimera, I would not recommend it for your 35 sequences -- instead use some sequence alignment program to align them, or get a sequence alignment for the proteins in that family from a database (if possible).  Some ways to get sequence alignments are listed here:
> <http://www.cgl.ucsf.edu/home/meng/sources.html>
> ... some sequence alignment webservers are listed at the bottom:
> <http://www.cgl.ucsf.edu/home/meng/sources.html#d>
> Chimera understands many sequence alignment formats, and sequence alignments are automatically shown in the Multalign Viewer tool. 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> You can open both files in Chimera (the 3D structure and the sequence alignment).  The structure should automatically associate with the alignment,
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association>
> but if it doesn't happen automatically, you can associate it manually using "Structure...Associations" in the sequence window menu.
> Then you can color the structure to show the conservation in the alignment, see "Structure.... Render by Conservation" in the sequence window menu.  There is also an example of conservation coloring at the bottom of this tutorial:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
> 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 Dec 3, 2012, at 10:18 PM, tao zhao wrote:
> > That's very kind of you, thank you very much!
> > I read the websites you gave me and can get a model from one sequence based on the templete now.
> > and what I really want to do is to construct a conserved model of all 35 sequences in this gene family.
> > The final picuture can have different colors in the different regions, showing various conservation.
> > I can't manage this right now.
> > Best regards
> > Tao
> > 
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