I have written a python script that takes an upstream result and outputs it as a pml script (series of PyMoL commands). When I run the file in pymol, some of the commands run, but the command line returns 'Invalid selection' Selector-Errors.
For instance. The script returns text lines such as:
fetch 3MPF
create 3MPFB63,3MPF and c. B and i. 63-68
remove 3MPF
align 3MPFB63, ref
When the script is run in PyMoL it says:
PyMOL>fetch 3MPF
please wait ...
PyMOL>create 3MPFB63,3MPF and c. B and i. 63-68
Selector-Error: Invalid selection name "3MPF".
( 3MPF and c. B and i. 63-68 )<--
PyMOL>remove 3MPF
Selector-Error: Invalid selection name "3MPF".
( 3MPF )<--
PyMOL>align 3MPFB63, ref
Selector-Error: Invalid selection name "3MPFB63".
3MPFB63<--
However, when those commands from the error are run individually, i.e. copying and pasting the snippet create 3MPFB63,3MPF and c. B and i. 63-68 the command runs perfectly well and makes the selection and creates the object.
Any help would be greatly appreciated.
It appears as if the answer to this problem is including async=0 in the fetch call, forcing the command-line to wait on the return from that command before executing the second command, i.e. it was trying to select objects before they existed.
For example,
fetch 3MPF, async=0
create 3MPFB63,3MPF and c. B and i. 63-68
delete 3MPF
align 3MPFB63, ref
This now works as intended. Will post back if down the line something else breaks when the full PML is auto-ran.
Classic, "as soon as you resort to asking on SO you figure it out," situation.