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<div>That's very kind of you, thank you very much!</div><div>I read the websites you gave me and can get a model from one sequence based on the templete now.</div><div>and what I really want to do is to construct a conserved model of all 35 sequences in this gene family.</div><div>The final picuture can have different colors in the different regions, showing various conservation.</div><div>I can't manage this right now.</div><div><br></div><div>Best regards</div><div>Tao</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><br><br><div><div id="SkyDrivePlaceholder"></div>> Subject: Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes<br>> From: meng@cgl.ucsf.edu<br>> Date: Mon, 3 Dec 2012 16:00:11 -0800<br>> CC: chimera-users@cgl.ucsf.edu<br>> To: zhaotaoshine@hotmail.com<br>> <br>> I forgot to say: you should use Chimera version 1.7 for these calculations. The Modell!
er interface has been improved since version 1.6, and the manual and tutorial links below describe version 1.7. <br>> <br>> Chimera 1.7 is available as snapshot and daily builds:<br>> <http://www.cgl.ucsf.edu/chimera/download.html#snapshots><br>> <http://www.cgl.ucsf.edu/chimera/download.html#daily><br>> <br>> Best,<br>> Elaine<br>> <br>> <br>> On Dec 3, 2012, at 3:56 PM, Elaine Meng wrote:<br>> <br>> > Hi Tao Zhao,<br>> > 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.<br>> > <br>> > 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:<br>> > <br>> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html><br>> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative><br>> > <br>> > ... 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":<br>> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches><br>> > <br>> > 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.<br>> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html><br>> > <br>> > I hope this helps,<br>> > Elaine<br>> > ----------<br>> > Elaine C. Meng, Ph.D. <br>> > UCSF Computer Graphics Lab (Chimera team) a!
nd Babbitt Lab<br>> > Department of Pharmaceutical Chemistry<br>> > University of California, San Francisco<br>> > <br>> > P.S. better to send questions about using Chimera to chimera-users@cgl.ucsf.edu (CC'd on this message), not chimera-dev@cgl.ucsf.edu which is meant for programmers<br>> > <br>> > On Dec 2, 2012, at 10:21 PM, tao zhao wrote:<br>> > <br>> >> Hello,<br>> >> 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.<br>> >> It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.<br>> >> <br>> >> Could you please give me some instruction?<br>> >> Thank you very much.<br>> >> <br>> >> Tao Zhao<br>> >> Northwest A&F University,Yangling, China<br>> > <br>> > <br>> > _____________________!
__________________________<br>> > Chimera-users mailing list<br>> > Chimera-users@cgl.ucsf.edu<br>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br>> <br></div> </div></body>
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