Dear Florian,
Sorry to hear that Ample isn't working for you.
I haven't seen this error before, but my initial guess would be that you're
trying to run Ample on Windows? If so then unfortunately the current release of
Ample isn't supported on Windows. Most of the work to port Ample to Windows has
been carried out, and it will be made available in a forthcoming release of
CCP4, but until then the only solution is to run Ample on Linux or Mac OSX.
If you're not running on Windows, please could you send me (off list) the file
debug.log, which should have been created in the directory:
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0
(the directory may be named ROSETTA_MR_0, ROSETTA_MR_1, ROSETTA_MR_2... etc.
depending on how many runs you have attempted.)
Just for information, at 197 residues your protein is on the large side
(although well within the bounds of what Ample is capable of solving), but 120
models is far fewer then we would normally recommend. The usual recommendation
is to make at least 1000 models.
Best wishes,
Jens
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Sauer
[florian.sau...@virchow.uni-wuerzburg.de]
Sent: 11 July 2014 08:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ample fails
Dear all,
I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197 residues
from 2.0 A data.
After the generation of initial (120) models by Rosetta (3.3) Ample stops with
the error-message below.
Could anyone provide me information about the origin of this error and possibly
how to solve the problem?
Thanks in advance for your replies!
Best wishes,
Florian
***
* Information from CCP4Interface script
***
The program run with command:
/home/flo/crystallography/ccp4-6.4.0/bin/ccp4-python -u
/home/flo/crystallography/ccp4-6.4.0/bin/ample -mtz
/home/flo/crystallography/Virchow/ESRF_20140707/CM133A/ccp4/pos5wedge3scaled.mtz
-fasta /home/flo/Desktop/arch.seq -name MVD0 -run_dir
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4 -nproc 3 -F
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -models_dir
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0/models/models_1
-early_terminate True -use_shelxe True -use_arpwarp False
has failed with error message
Traceback (most recent call last):
File /home/flo/crystallography/ccp4-6.4.0/bin/ample, line 757, in
ensemble.create_ensembles( amopt.d )
File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py,
line 85, in create_ensembles
ensembles = ensemble_models( amoptd['spicker_results'][ cluster-1
].pdb_list, amoptd, ensemble_id=cluster )
File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py,
line 58, in ensemble_models
percent=amoptd['percent'] )
File
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py,
line 168, in generate_ensembles
self.make_truncated_ensembles()
File
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py,
line 312, in make_truncated_ensembles
clusterer.generate_distance_matrix( self.truncated_models[tcount] )
File
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/cluster_with_MAX.py,
line 55, in generate_distance_matrix
retcode = ample_util.run_command( cmd, logfile=log_name )
File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_util.py,
line 274, in run_command
p = subprocess.Popen( cmd, stdin=stdin, stdout=logf,
stderr=subprocess.STDOUT, cwd=directory, **kwargs )
File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line
711, in __init__
errread, errwrite)
File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line
1308, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
***
--
Dr. Florian Sauer
Rudolf Virchow Zentrum für Experimentelle Biomedizin
Josef-Schneider-Str. 2, Haus D15
97080 Würzburg
