[PyMOL] Bond command not functioning in script

[Stuart B. <srb...@wi...>]

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