CODEWITHSUNDEEP
pythonpython-2.7scriptingpymol
Lyk
Lyk

Reputation: 33

Why does a pymol (pml) script generated by python not run correctly in PyMoL?

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.

Upvotes: 0

Views: 2380

Answers (1)

Lyk
Lyk

Reputation: 33

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.

Upvotes: 1

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