Re: [ccp4bb] AMPLE failure

2014-07-14 Thread Ronan Keegan 

Hi Robert,

Thanks for your interest in AMPLE and reporting this bug. There is a 
small bug that has come about as a result of the latest MRBUMP update 
last week that causes this problem. We're preparing a fix for it which 
should be in the next ccp4 update towards the end of this week or early 
next week. In the meantime I can send you (off list) the latest version 
of the code that you can manually install.


Best wishes,

Ronan

On 12/07/14 18:58, Robert Kirchdoerfer wrote:

Hi,

I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu.  It looks like it 
found all the program dependencies that it needs and Rosetta looks like it ran 
okay and I think MRBUMP looks alright, but then the program stopped with the 
following error message:

MR and shelx DONE

  ALL DONE  (in 1.64101706141 hours)



Saved results as file: 
/home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl


***
* Information from CCP4Interface script
***
The program run with command: 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz 
/home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta 
/home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 
-run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True 
-rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -early_terminate True   
-use_shelxe True -use_arpwarp False
has failed with error message
Traceback (most recent call last):
   File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, 
line 838, in
 summary = amopt.final_summary()
   File 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py,
 line 197, in final_summary
 result_summary.append( getattr( result, title2attr[ h ] )  )
KeyError: 'SHELXE_ACL'

Any thoughts on how I might troubleshoot this?

Thanks and Best wishes,
Rob


--
Scanned by iCritical.

Re: [ccp4bb] AMPLE failure

2014-07-12 Thread Thomas, Jens 
Dear Rob,

Sorry to hear that this issue has affected you - it's a known bug which will be 
fixed in the next ccp4 update.

AMPLE has run to completion but crashed printing out the results.

To see the results, you can run the following command at the terminal 
(command-line):

/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python  
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/mrbump_results.py
 /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/MRBUMP/cluster_1

If that doesn't work or you need any additional help, please contact me 
off-list.

Best wishes,

Jens



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert 
Kirchdoerfer [rkirc...@scripps.edu]
Sent: 12 July 2014 18:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AMPLE failure

Hi,

I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu.  It looks like it 
found all the program dependencies that it needs and Rosetta looks like it ran 
okay and I think MRBUMP looks alright, but then the program stopped with the 
following error message:

MR and shelx DONE

 ALL DONE  (in 1.64101706141 hours)



Saved results as file: 
/home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl


***
* Information from CCP4Interface script
***
The program run with command: 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz 
/home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta 
/home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 
-run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True 
-rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -early_terminate True   
-use_shelxe True -use_arpwarp False
has failed with error message
Traceback (most recent call last):
  File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, 
line 838, in
summary = amopt.final_summary()
  File 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py,
 line 197, in final_summary
result_summary.append( getattr( result, title2attr[ h ] )  )
KeyError: 'SHELXE_ACL'

Any thoughts on how I might troubleshoot this?

Thanks and Best wishes,
Rob