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

Maja Divjak divjak.m at wehi.EDU.AU
Fri Oct 18 02:26:32 PDT 2013


Hello again Elaine,

And further to that, how do I put the two molecules together please, now that I have a possible propeptide for IL-1beta? I had a go using MatchMaker with best-aligning pair of chains and everything else at default, but I'm not sure if this is the best approach? The propeptide bound via it's N-terminus to the C-terminus of IL-1 (in rainbow depiction) and the propeptide is supposed to be at the N-terminus of the whole. Apologies it this seems totally lame, but protein structure is not my forte...

I look forward to your reply,

Thank you and best wishes,

Maja

On Oct 18, 2013, at 7:28 PM, Maja Divjak wrote:

> 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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