Re: [ccp4bb] Refmac buccaneer combination
Can you send me the rest of the logfile? I think I've seen an error like this where the number of atoms built dropped to zero, in which case there is something seriously wrong with the input phases. But I expect there are other ways to trigger a refmac fail - I can't tell for sure without more information. Thanks, Kevin On 17 March 2014 22:12, Debajyoti Dutta debajyoti_dutt...@rediffmail.comwrote: Hi all, I am running autobuild and refinement in buccaneer/refmac pipeline. Does anybody have any idea about the following error . Refmac_5.8.0069: Check input coordinates Traceback (most recent call last): File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in control.run_program_template( refmac_all ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 740, in run_program_template self.run_program( prgm, argx, cmdx ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 729, in run_program raise( StandardError( 'Fail in program '+prgm+'' ) ) StandardError: Fail in program Thanks in advance. Best Debajyoti http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? Get your own *FREE* website, *FREE* domain *FREE* mobile app with Company email. *Know More *http://track.rediff.com/click?url=___http://businessemail.rediff.com/company-email-hosting-services?sc_cid=sign-1-10-13___cmp=hostlnk=sign-1-10-13nsrv1=host -- EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] Refmac buccaneer combination
Hi Ronan and Kavin, I checked the input files and found that i was assigning wrong column labels in buccaneer for which the error was popping up. I was able to fix it now. Thanks a lot. Debajyoti On Tue, 18 Mar 2014 21:09:15 +0530 wrote Hi Debajyoti, Thanks for sending the file. It's clearly a problem for Buccaneer to build anything into the map you've provided it with. It fails to find any residues and as a result the output PDB file from Buccaneer is empty. Refmac then complains about 0 atoms. Is it poor map that you are providing? It might help if you provide it with a starting model to build from, e.g. a molecular replacement solution. Otherwise try ARP/wARP wit the same data. Best wishes, Ronan On 18/03/14 21:41, Debajyoti Dutta wrote: Hi Ronan, Please find the log file attached. Thanks for your reply. Best Debajyoti On Tue, 18 Mar 2014 16:03:18 +0530 wrote Hi Debajyoti, This is a problem with the PDB file that Buccaneer is passing to Refmac for refinement. It's possible that Buccaneer couldn't build anything into the map in which case the PDB file will have no coordinates in it and Refmac will fail as a consequence. However, to make a proper assessment of the problem it would be best if you could send us the entire Buccaneer log file for the job. Best wishes, Ronan On 18/03/14 07:12, Debajyoti Dutta wrote: Hi all, I am running autobuild and refinement in buccaneer/refmac pipeline. Does anybody have any idea about the following error . Refmac_5.8.0069: Check input coordinates Traceback (most recent call last): File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in control.run_program_template( refmac_all ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 740, in run_program_template self.run_program( prgm, argx, cmdx ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 729, in run_program raise( StandardError( 'Fail in program ' ) ) StandardError: Fail in program Thanks in advance. Best Debajyoti Get your own FREE website, FREE domain FREE mobile app with Company email. Know More -- Scanned by iCritical. Get your own FREE website, FREE domain FREE mobile app with Company email. Know More -- Scanned by iCritical.
[ccp4bb] Refmac buccaneer combination
Hi all, I am running autobuild and refinement in buccaneer/refmac pipeline. Does anybody have any idea about the following error . Refmac_5.8.0069: Check input coordinates Traceback (most recent call last): File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in control.run_program_template( refmac_all ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 740, in run_program_template self.run_program( prgm, argx, cmdx ) File /Applications/ccp4-6.4.0/share/python/CCP4pipeline.py, line 729, in run_program raise( StandardError( 'Fail in program ' ) ) StandardError: Fail in program Thanks in advance. Best Debajyoti
