[Chimera-users] How to make trimer by Chimara?

[Elaine Meng]

Dear Wisoot Chanit,
If you’re using ChimeraX there is another address:  chimerax-users at cgl.ucsf.edu

Besides the ChimeraX Modeller tool link I sent earlier
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
… there is also an example here
<http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller>

Also we are not the Modeller developers, so depending on the question you may need to look at the Modeller help at their website:  
<https://salilab.org/modeller/discussion_forum.html>

Best,
Elaine

> On Nov 23, 2019, at 9:39 AM, Wisoot Chanit <wchanit at yahoo.com> wrote:
> 
> Dear Dr.Eliane Meng,
> 
> Thank you very much for your reply and recommendations, which are really helpful. I have tried using ChimeraX a few days ago. It is very simpler than Chimera. By following the instructions you recommended, I believe I can make it although it may take some time and effort as you mentioned. I used to use Modeller 5-6 years ago for my Ph.D. papers and now I need to go back to my knowledge. If I have questions, I will send it directly to chimera-users at cgl.ucsf.edu . 
> 
> Thank you very much again for this help.
> 
> Wisoot Chanit 
> 
> On Sunday, November 24, 2019, 12:19:19 AM GMT+7, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 
> Dear Wisoot Chanit,
> It is recommended to send Chimera questions to chimera-users at cgl.ucsf.edu (CC’d here).
> 
> As mentioned in the manual page, the Modeller interface in Chimera can only be used to make monomers.  Although Modeller by itself can model multimers, the GUI to run it in Chimera is simpler and only has the most common options.
> 
> So if you are using Chimera, you could first model a monomer and save it to a file.  Then you could open 3 copies of that monomer model and match them onto the 3 chains in a trimer structure. There is a manual page for the Modeller tool in Chimera and also a tutorial with an example.  See also the manual page on superposition (matching structures in 3D).
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> 
> Our newer ChimeraX program has an improved Modeller interface that can model a trimer, however, if the template is a trimer.  So another possibility is to use the ChimeraX program instead of Chimera.
> <http://www.rbvi.ucsf.edu/chimerax/>
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
> 
> Yet another possibility is to download Modeller and learn how to use it directly, but that would take more time and effort.
> <https://salilab.org/modeller/>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> 
> > On Nov 23, 2019, at 6:10 AM, Wisoot Chanit <wchanit at yahoo.com> wrote:
> > 
> > Dear Dr.Elaine Meng,
> > 
> > I am a new user of Chimera and have been searching for methods to do comparative modeling of rotavirus structure. 
> > 
> > I have read your post (CCL: Monomer to Trimer), but I still questions. 
> > 
> > My aim is to make a homology modeling protein of VP7 protein of rotavirus using 3FMG pdb as a template. I do not know how to impose three monomers into the template. 
> > 
> > My amino acid sequence is 
> > 
> > Rotavirus G3 :
> > TSTLCLYYPSEAATEINDNSWKDTLSQLFLTKGWSTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDATTFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSK
> > 
> > Could you please guide me how I can find a protocol to make a homology model? I tried to follow the attached paper. 
> > 
> > Thank you very much.
> > 
> > Sincerely,
> > Wisoot Chanit
> > 
> > 
> > 
> > 
> > CCL: Monomer to Trimer
> 
> > 
> > 
> > 
> > <High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014.pdf>
>