Stuart,
For what's it's worth, I'm not able to reproduce the problem:
Aside from automatic suppression of output when using the Python API,
I'm getting the exact same behavior with
# test1.pml
cmd.pseudoatom("temp",pos=[0,0,0],name="A")
cmd.pseudoatom("temp",pos=[0,0,5],name="B")
cmd.bond("temp////A","temp////B")
# test2.pml
pseudoatom temp,pos=[0,0,0],name=A
pseudoatom temp,pos=[0,0,5],name=B
bond temp////A,temp////B
# and test3.pml
python
cmd.pseudoatom("temp",pos=[0,0,0],name="A")
cmd.pseudoatom("temp",pos=[0,0,5],name="B")
cmd.bond("temp////A","temp////B")
python end
Cheers,
Warren
________________________________
From: Stuart Ballard [mailto:[email protected]]
Sent: Monday, September 21, 2009 3:53 PM
To: pymol-users
Subject: [PyMOL] Bond command not functioning in script
Hello all, Warren,
I have a script which creates two pseudoatoms and a bond object
between them, but the bond step consistently fails. However, the two
pseudoatoms can be bound in the console after the script halts with the
exact same command which fails in the script:
cmd.bond("temp0////A0","temp0////B0")
Alternatively, cmd.do("bond temp0////A0, temp0////B0") fails
just the same.
The following works perfectly:
PyMOL>python
1:cmd.pseudoatom("temp",pos[0,0,0],name="A")
2:cmd.pseudoatom("temp",pos[0,0,5],name="B")
3:cmd.bond("temp////A","temp////B")
PyMOL>python end
So can anyone tell me why the exact same thing in a script halts
after 2?
Thanks,
Stuart Ballard
Dept. of Biochemistry
University of Wisconsin-Madison
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