Re: [PyMOL] Problem with pymol

[Thomas H. <tho...@sc...>]

Hi Roger,

Looks like Open3dQSAR tries to use a pipe to communicate with PyMOL. That is possible with "PyMOLWin.exe +2", with "PyMOLWinWithConsole.bat" and with "Scripts\pymol.exe". I suggest that you try this:

env pymol="C:\Users...\PyMOLWinWithConsole.bat"

Hope that helps.

Cheers,
  Thomas

> On Mar 21, 2021, at 8:26 PM, Roger Vuong <rog...@bo...> wrote:
> 
> Hi,
> I am using Open3DQSAR and I am having trouble getting molecules to show in pymol using an educational license. In Open3DQSAR I am able to change the executable using the env pymol command, I then change the directory, then import the sdf file, and pymol opens but pymol does not show the molecules. The error points to a python script in pymol and states
> Traceback (most recent call last):
> File "C:\Users\roger\Appdata\Local\Schrodinger\Pymol2\lib\site-packages\pymol\parser.py", line 52, in stdin_reader
> 1 = sys.stdin.readline()
> AttributeError: 'NoneType' object has no attribute 'readline'
> Screenshots are attached below. Do you have a solution to fix this problem?
> Thanks,
> Roger 
> <image.png>
> <image.png>
> <image.png>
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.