[Chimera-users] Create a protein model using Chimera?
divjak.m at wehi.EDU.AU
Fri Oct 18 01:28:59 PDT 2013
Thanks for the reply. I ended up using Modeler, which after much frustration, gave me some reasonable models.
Thank you and best wishes,
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.
> 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 :
> 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
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
More information about the Chimera-users