Hello,
We are currently in the final stages of updating the standalone version of
pdb_extract.
In the meantime, we encourage users to try the web server version of the program at
http://pdb-extract.rcsb.org/
The PDB_extract will:
# provide you with an author information form, which can be saved/updated for
multiple related entries
# assemble coordinate and log files pertaining to your specific experimental
methods
# allow you to "fix" the primary sequence of your protein/nucleotide chains to account for
unresolved residues
# output the coordinate (and structure factor files, if applicable) in mmCIF format for Validation
and for deposition at RCSB ADIT or PDBj ADIT.
If the web version produces similar errors, please email the log file to use at
depo...@deposit.rcsb.org and we will look into it.
Sincerely,
Jasmine
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 <http://Jan.Abendroth_at_gmail.com>
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com
--
====================================================================
Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087
Email: jas...@rcsb.rutgers.edu
Phone: (732)-445-0103
Fax: (732)-445-4320
====================================================================
