Arch Linux

Description:

In PyMOL 1.8.6.0 (currently in testing), the peptide sequence generation command ("pymol.cmd.fab") breaks when called from a python shell. I presume this might be related to problems when porting to python 3.


Additional info:
* package version(s)
* config and/or log files etc.


Steps to reproduce:

From a python 3 shell (or script), issue the following commands:

>>> import pymol
>>> pymol.finish_launching() # A PyMOL windows open
>>> pymol.cmd.fab("EEG")
Traceback (most recent call last):
File "", line 1, in <module>
SystemError: error return without exception set
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.6/site-packages/pymol/editor.py", line 427, in fab
state,dir,hydro,ss,quiet,_self)
File "/usr/lib/python3.6/site-packages/pymol/editor.py", line 392, in _fab
attach_amino_acid("pk1",code[sequence.pop()],animate=0,ss=ss,hydro=hydro,_self=_self)
File "/usr/lib/python3.6/site-packages/pymol/editor.py", line 210, in attach_amino_acid
tmp[0] = str(tmp[0]+1) # counting up
TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'


Using the same on a python 2 terminal with PyMOL 1.8.4.0 (community) produces no errors and peptide with sequence "EEG" is successfully generated in PyMOL.