Hi Jan,
Have you tried using the xxxxx.refmac file that is created instead of the log file. It is in cif format and may be in the "DepositFiles" directory.
Hope you are well and talk to you later,
Eric
================================
Eric T. Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
email: [log in to unmask]
================================
On Wed, 27 Jul 2011, Jan Abendroth wrote:
>Hi all,
>we typically use pdb_extract to generate pdb files with a good header.
>There seems to be an issue with logfiles from refmac5.6.0117, distributed with the current ccp4 version, and pdb_extract.
>
>pdb_extract version-3.006 is distributed with ccp4-6.2.0. While reading the refmac log file, pdb_extract chokes with a segmentation fault. When run
>without reading in the refmac log file, the program complains about the following missing link, both in the linux and osx distribution of ccp4.
>
>Can not open file (/usr/local/ccp4/ccp4-6.2.0/ccp4-6.2.0//src/harvest_app_/pdb_extract/pdb-extract-data/mmcif_pdbx_2.items) in get_lines_from_file
>
>pdb_extract version-3.010, as downloaded form the rcsb webpage also chokes on the refmac5 logfile with a segmentation fault.
>
>Any ideas how to treat the new refmac log files in pdb_extract?
>
>Thanks a lot.
>Jan
>
>
>--
>Jan Abendroth
>Emerald Biostructures
>Seattle / Bainbridge Island, WA, USA
>home: Jan.Abendroth_at_gmail.com
>work: JAbendroth_at_embios.com
>http://www.emeraldbiostructures.com
>
>
>
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