[Chimera-users] Create a protein model using Chimera?

Maja Divjak divjak.m at wehi.EDU.AU
Fri Oct 18 01:28:59 PDT 2013


Hi Elaine,

Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models.

Thank you and best wishes,

Maja

On Oct 18, 2013, at 3:29 AM, Elaine Meng wrote:

> Dear Dr Maja Divjak,
> Sorry, Chimera does not do de novo modeling.  Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
> 
> I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling.  I have not done it myself, so I don't have any specific recommendations.  Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net :
> <http://ccl.net/cgi-bin/ccl/send_ccl_message>
> Best,
> 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 Oct 16, 2013, at 12:04 AM, Maja Divjak <divjak.m at wehi.EDU.AU> wrote:
> 
>> Hello Chimera,
>> 
>> I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family. 
>> 
>> I look forward to your reply!
>> 
>> Thank you and best wishes,
>> 
>> Dr Maja Divjak,
>> WEHI, Melbourne, Australia
> 

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