[Chimera-users] Help

[Kimberley Perry]

I will look into that. I am a Physical Chemist now, and my PhD requires a
Python Coding course. Everything just has to be done in there. So, I have
to write a code to convert the .xyz file to a .pdb and have Chimera (I was
hoping) to show the structures.

On Tue, May 8, 2018 at 10:43 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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>_______________________________________________
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