For example, PDB 1cex results in the following in Open-Source PyMOL 1.7.6.0 and PyMOLProbity version 0.1 (25fd078)
PyMOL>fetch 1cex
[...]
PyMOL>reduce_obj 1cex
WARNING: A 213 SER N H atom too close to A 212 GLY C by 0.0107972A
you may need to adjust using -METALBump or -NONMETALBump.
INFO:pmg_tk.startup.pymolprobity_dev.main:Generated Reduce output with flips for '1cex'.
INFO:pmg_tk.startup.pymolprobity_dev.main:Processed Reduce output to extract list of flips.
ERROR:pmg_tk.startup.pymolprobity_dev.main:get_object: '1cex' not in plugin objects dict.
PyMOL>flipkin_obj 1cex
Skipping iteration; node with all states disabled
Skipping iteration; node with all states disabled
INFO:pmg_tk.startup.pymolprobity_dev.main:Generated Flipkin output for '1cex'.
Traceback (most recent call last):
File "/usr/local/Cellar/pymol/1.7.6.0_1/libexec/lib/python2.7/site-packages/pymol/parser.py", line 256, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
File "/Users/jared/.pymol/startup/pymolprobity_dev/main.py", line 724, in flipkin_object
o.kin['flipkinNQ'] = process_flipkin_output(flipkinNQ_raw)
File "/Users/jared/.pymol/startup/pymolprobity_dev/main.py", line 601, in process_flipkin_output
return kinemage.process_kinemage(kinstr)
File "/Users/jared/.pymol/startup/pymolprobity_dev/kinemage.py", line 327, in process_kinemage
data = KEYWORD_HANDLERS[base_keyword](lines, copy.copy(context))
File "/Users/jared/.pymol/startup/pymolprobity_dev/points.py", line 680, in process_vectorlist
vectors = _parse_bonds_vectorlist_body(lines[1:])
File "/Users/jared/.pymol/startup/pymolprobity_dev/points.py", line 603, in _parse_bonds_vectorlist_body
b = float(atom_sel[20:27].replace('B', ''))
ValueError: invalid literal for float(): 9.22 t
This happens regardless of whether Flipkin is using latest probe or phenix.probe.
The atom info string format that causes the above error is
og aser A 120 0.73B9.22 tmpcA2P6n
(note leading space), where tmpXXX is the temporary file name created as input to Probe.
For example, PDB 1cex results in the following in Open-Source PyMOL 1.7.6.0 and PyMOLProbity version 0.1 (25fd078)
This happens regardless of whether Flipkin is using latest
probe
orphenix.probe
.The atom info string format that causes the above error is
(note leading space), where tmpXXX is the temporary file name created as input to Probe.