Chimera, Modeller, and socket modules
Hello, I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.
Hi Casey, I guess the question is what Python interpreter is being used by Modeller. To get more information, insert these lines before the "from modeller.parallel import *" line in LoopRefinement_3cpu.py: import sys print(sys.executable) print(sys.version) Let me know what the output is. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 31, 2020, at 3:55 PM, Casey Becker <cbecker11@mail.csuchico.edu> wrote:
Hello,
I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.
<LoopRefinement_3cpu.py><myloop.py><reply>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Okay, looking at the reply you got on the Modeller mailing list, I understand the issue better. The Modeller executable is a Python interpreter, but ships with none of the standard modules, such as 'socket'. To get this to work you need to use Chimera's full-fledged Python interpreter as the executable as the first step. So the executable location should be "C:\Program Files\Chimera 1.14\bin\python.exe" (you should double check that this is correct on your machine -- I don't have access to a Windows machine at this time). Before you run Modeller you need to add the Modeller library to Python's path so that it will find the "modeller" module. You should do this in your script before Modeller tries to import its own modules with these lines: import sys sys.path.insert(0, r"C:\Program Files\Modeller9.24\modlib") --Eric
On Aug 31, 2020, at 5:33 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Casey, I guess the question is what Python interpreter is being used by Modeller. To get more information, insert these lines before the "from modeller.parallel import *" line in LoopRefinement_3cpu.py:
import sys print(sys.executable) print(sys.version)
Let me know what the output is.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Aug 31, 2020, at 3:55 PM, Casey Becker <cbecker11@mail.csuchico.edu> wrote:
Hello,
I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.
<LoopRefinement_3cpu.py><myloop.py><reply>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Casey Becker -
Eric Pettersen