Is the get-pip.py file in the directory that you are running the command from? —Eric
On Mar 28, 2024, at 5:34 AM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Eric,
I've added chimera to my path. When I enter the command, I get a "no such script" error. I made sure pip is properly installed, as you can see up above the error.
Thanks,
Garrett Scapellato
Research Technician II Edwards Lab DHVI Duke University
<Outlook-zzxnlpfg.jpg> From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Wednesday, March 27, 2024 4:15 PM To: Garrett Scapellato <garrett.scapellato@duke.edu <mailto:garrett.scapellato@duke.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Importing Modules into Chimera
If chimera is not on your path, you will have to specify the full path to the chimera executable. See this page: Chimera Startup and Input <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/startup.html> for info about where the chimera executable should be on your system.
--Eric
On Mar 27, 2024, at 1:09 PM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Eric,
That was the first thing I tried. I received this error:
"(base) DHVI-F5KJC04Q:pythonProject edwardslab$ chimera --nogui --script get-pip.py -bash: chimera: command not found
Thanks,
Garrett Scapellato
Research Technician II Edwards Lab DHVI Duke University
<Outlook-uz4k02ar.jpg> From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Wednesday, March 27, 2024 4:07 PM To: Garrett Scapellato <garrett.scapellato@duke.edu <mailto:garrett.scapellato@duke.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Importing Modules into Chimera
You do not put "chimera --nogui --script get-pip.py" into a Python file and execute it using your system python3. You execute the command directly in the Unix shell.
--Eric
On Mar 27, 2024, at 12:18 PM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
This error, the first one in the previous email.
Garrett Scapellato
Research Technician II Edwards Lab DHVI Duke University
<Outlook-5psmrh0k.jpg> From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Wednesday, March 27, 2024 1:59 PM To: Garrett Scapellato <garrett.scapellato@duke.edu <mailto:garrett.scapellato@duke.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Importing Modules into Chimera
Hi Garrett, Using your system installer will not install pandas into Chimera's Python interpreter, which is why you need to install pip into Chimera with the get-pip.py script. You do that with "chimera --nogui --script get-pip.py" from the Unix shell, not from within Chimera. What happened when you tried it from the Unix shell?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 27, 2024, at 9:59 AM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Eric,
I've tried installing pip to chimera using that code both in my terminal and in chimera, but I get syntax errors. Just in case it is important, I will note that I skipped the first step of installing the pip installer, because my computer already has a python pip installer.
Thanks,
Garrett Scapellato
Research Technician II Edwards Lab DHVI Duke University
<Outlook-f2ju1yow.jpg> From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Sent: Friday, March 22, 2024 4:22 PM To: Garrett Scapellato <garrett.scapellato@duke.edu <mailto:garrett.scapellato@duke.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Importing Modules into Chimera
Hi Garrett, Chimera has its own Python interpreter, so installing pandas into other Python interpreters on your machine will not make available in Chimera. You should be able to install pandas into Chimera's interpreter by following the instructions in this older mailing-list message: Re: [Chimera-users] How to install package in chimera python? - Chimera-users - RBVI Mailing Lists <https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/message/F7PH7EM6HIQNGKVWWLS3CPEPSU2MLURU/>
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 22, 2024, at 12:29 PM, Garrett Scapellato via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Chimera Help,
Hello, I hope you are doing well. I am attempting to use the "pandas" module while using Chimera to read python code. I receive this error any time I do. I am able to use pandas while using other python interpreters on my computer. I am also able to use other modules, such as NumPy when using Chimera to run python code. Any help in this issue would be greatly appreciated.
Thank you for your time,
Garrett Scapellato
Research Technician II Edwards Lab DHVI Duke University
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