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 [[email protected]] on behalf of Florian Sauer [[email protected]] Sent: 11 July 2014 08:37 To: [email protected] 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
