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 <rogervu...@boisestate.edu> 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> > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
