Without seeing the file it's hard to be definite, but the syntax error
one line after the end of the file might suggest that some multi-line
text earlier in the file is missing its closing '<newline><semicolon>'
terminator.
Regards,
Peter.
On 25/09/2019 15:00, [email protected] wrote:
Dear ccp4ers,
I have refined several structures using refmac5 within ccp4i and tried to
upload the output mmcif files to the pdb in order to deposit the
coordinates/structure factors.
However, during the initial upload process when the files are scanned I get the
following errors:
ERROR - Read file 'input_file_1' failed:
syntax error at line 30421
ERROR - syntax error at line 30426
Warning - Duplicate category name chem_comp_atom at line 30428
Warning - Duplicate category name chem_comp_bond at line 30446
Warning - Duplicate category name chem_comp_angle at line 30467
ERROR - syntax error at line 30581
ERROR - syntax error at line 30585
These all lie after the coordinates in the dictionary part of the file. When I
have investigated this I cannot see any duplicated category names that would
result in the above warnings and the syntax errors are not a result of anything
obvious. I have checked for hidden characters, found none, and can see nothing
else wrong. Finally, line 30585 does not exist, the file stops at 30584.
Has anyone had similar problems or any suggestions that might solve this?
Thanks,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email [email protected]
tel 01235 567717
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