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.
