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

tao zhao zhaotaoshine at hotmail.com
Mon Dec 3 22:18:53 PST 2012


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 regardsTao







> Subject: Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes
> From: meng at cgl.ucsf.edu
> Date: Mon, 3 Dec 2012 16:00:11 -0800
> CC: chimera-users at cgl.ucsf.edu
> To: zhaotaoshine at hotmail.com
> 
> I forgot to say:  you should use Chimera version 1.7 for these calculations.  The Modeller interface has been improved since version 1.6, and the manual and tutorial links below describe version 1.7.  
> 
> Chimera 1.7 is available as snapshot and daily builds:
> <http://www.cgl.ucsf.edu/chimera/download.html#snapshots>
> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
> 
> Best,
> Elaine
> 
> 
> On Dec 3, 2012, at 3:56 PM, Elaine Meng wrote:
> 
> > Hi Tao Zhao,
> > Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program.  To use this feature, you would first need to go to the Modeller web site and sign up for  a license key <http://www.salilab.org/modeller/registration.html>  -- it is free for noncommercial use.
> > 
> > A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see:
> > 
> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
> > 
> > ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template":
> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
> > 
> > There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it.
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.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
> > 
> > P.S. better to send questions about using Chimera to chimera-users at cgl.ucsf.edu (CC'd on this message), not chimera-dev at cgl.ucsf.edu which is meant for programmers
> > 
> > On Dec 2, 2012, at 10:21 PM, tao zhao wrote:
> > 
> >> Hello,
> >> I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family.
> >> It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.
> >> 
> >> Could you please give me some instruction?
> >> Thank you very much.
> >> 
> >> Tao Zhao
> >> Northwest A&F University,Yangling, China
> > 
> > 
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
 		 	   		  
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