[Chimera-users] Help

[Elaine Meng]

Hi Kim,
Not sure why you are using python here, but then again I’m not a python programmer myself.

Generally for antibody-antigen modeling, you would just open the 3D structures from PDB or mmCIF files, then use the various analysis tools in Chimera (FindHBond, etc.).  If you don’t already have 3D structures of these proteins, one approach is to “homology” model them from known structures of similar sequences.  You could use Chimera’s Modeller interface for comparative modeling to do that.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>

However, even if you had models of 3D structures of both proteins, Chimera will not predict how the two will interact.  For that, you would need to use some other program for protein-protein docking.

I hope this helps,
Elaine

> On May 7, 2018, at 7:48 PM, Kimberley Poland <knperry at go.olemiss.edu> wrote:
> 
> Thank you for the response. Ab and Ag are not elements in this project-Ab not at all.  They are referencing antigens and antibodies. I was creating a skeleton for my specific project but decided to try the template I found first to see what should happen. I wanted to see the interface of an antigen and an antibody. 
> 
> Kimberley N. Poland, AA, BA, BA, MS
> Doctoral Student
> Department of Chemistry & Biochemistry
> Coulter Hall Room 283
> 601-692-8577
> 
> On May 7, 2018, at 5:26 PM, David Gae <ddgae at ucdavis.edu> wrote:
> 
>> Dear Kim, 
>> 
>> I think you have a typo- you are missing () after your object createAb
>> 
>> Btw, like Dr. Meng said it is really confusing what you are trying to do because the script you provided is for a  water molecule.
>> 
>>> On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry at go.olemiss.edu> wrote:
>>> 
>>> Elaine, thank you so much for responding to me! Granted, I am new to Python, but I have a biochemistry (undergrad degree) and physical chemistry (working on PhD now) working knowledge. I would like to look at the interactions of Ab and Ag as they may apply to drug discovery. It is for a final project in Python, which I've only had one semester of. I downloaded Chimera according to your instructions. I ran the .py file without error, but a visual never displays.
>>> 
>>> Kim
>>> 
>>> On Mon, May 7, 2018 at 10:15 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Hi Kim,
>>> I have no idea what you mean by “your online water example” as it doesn’t sound like something we wrote… would need much more information on what you did, and what you were trying to do, to be able to comment on whether it was right or not.
>>> 
>>> The Chimera tutorials are here and/or in the Chimera Help menu:
>>> 
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
>>> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
>>> <http://www.rbvi.ucsf.edu/chimera/tutorials.html>
>>> 
>>> Good luck,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>> > On May 6, 2018, at 7:11 PM, Kimberley Perry <knperry at go.olemiss.edu> wrote:
>>> > 
>>> > Hello! I am trying to model molecular structures for a Python course I am taking. I tried your online water example, and it looked like it ran, but I am not seeing the structure. Am I doing something wrong?
>>> > 
>>> > Kim
>>> 
>>> 
>>> <Final Exam.py>_______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users