Dear Elaine and Eric,
Really appreciate your kind help! Sorry for the late reply. We were busy on the other project.
Our volunteer Kevin modified Eric's python script. Then we execute the remote
headless Chimera by the command "
chimera", and "open recoding_movie_kevin.py"
The following error message will pop out
:
> open /work/02444/drugsu/recoding_movie_kevin.py
Executing /work/02444/drugsu/recoding_movie_kevin.py...
Reading Amber prmtop
Done reading Amber prmtop
Creating interface
Creating bonds
Bonds created
Assigning chain ID A to 259 residues, e.g. GLY
Model 2 (AAA_with_AAA_91_12A_prod_v0_l1.mdcrd) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
energy cutoff -0.5
minimum helix length 3
minimum strand length 3
Use command 'help ksdssp' for more information.
Computing secondary structure assignments...
Computed secondary structure assignments (see reply log)
Interface created
Traceback (most recent call last):
File "/work/02444/drugsu/chimera_headless/share/ReadStdin/__init__.py", line 79, in _runCommand
chimera.runCommand(cmd)
File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand
makeCommand(*args, **kw)
File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand
f(c, args)
File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1570, in doOpen
modelArg, noprefs)
File "<string>", line 1, in <module>
File "/work/02444/drugsu/chimera_headless/share/Midas/__init__.py", line 2090, in open
noprefs=noprefs)
File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1817, in open
models = func(filename, *args, **kw)
File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 1196, in _openPython
loadFunc(sandboxName, fileName, f)
File "recoding_movie_kevin.py", line 39, in <module>
runCommand('preset apply pub 1')
File "/work/02444/drugsu/chimera_headless/share/chimera/__init__.py", line 2608, in runCommand
makeCommand(*args, **kw)
File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 69, in makeCommand
f(c, args)
File "/work/02444/drugsu/chimera_headless/share/Midas/midas_text.py", line 1676, in doPreset
mgr.applyPreset(type, vals[1])
File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 107, in applyPreset
func()
File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 36, in <lambda>
lambda:preset(publication=True, depthCued=False), False)
File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset
with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()):
AttributeError: 'module' object has no attribute 'update'
AttributeError: 'module' object has no attribute 'update'
File "/work/02444/drugsu/chimera_headless/share/chimera/preset.py", line 183, in preset
with nested(NA.blockUpdates(), chimera.update.blockFrameUpdates()):
See reply log for Python traceback.
If we use the GUI chimera and open this script, it will work properly. We have searched the mailing list but didn't see similar error messages. If not too much asking, could you kindly offer some solutions? Please forgive any ignorance, if any.