Hi Kim, Again, I do not know what instructions or python file you mean. If you just meant you were trying to download and install Chimera on Linux, the instructions say: "Some browsers may download the file as chimera-get.py. If yours does, rename the file to chimera-installer.bin” <http://www.rbvi.ucsf.edu/chimera/data/downloads/1.11/linux.html> (… and see also further instructions on that page, e.g. it mentions a “couldn’t get visual” error) However, Chimera doesn’t have any force field calculations that include Ag, and Ab isn’t even an element as far as I know, so you may be barking up the wrong tree. <https://en.wikipedia.org/wiki/Symbol_(chemistry)#Symbols_and_names_not_curre...> Good luck, Elaine
On May 7, 2018, at 8:20 AM, Kimberley Perry <knperry@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@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@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
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