Greetings,
We have T-COFFEE_distribution_Version_13.39.0.d675aed.tar.gz installed.
It is activated as an LMOD module which was configured like this:
(script to configure is here:
ftp://newsaf.bio.caltech.edu/pub/software/linux_or_unix_tools/module_generate_from_directory.sh
)
TOPDIR=/usr/common/modules/el7/x86_64/software/t-coffee/13.39.0-CentOS-vanilla
module_generate_from_directory.sh \
t-coffee \
13.39.0 \
CentOS/vanilla \
$TOPDIR \
"A collection of tools for Computing, Evaluating and Manipulating
Multiple Alignments of DNA, RNA, Protein Sequences and Structures." \
"
http://www.tcoffee.org/"
cat
>>/usr/common/modules/el7/x86_64/modules/all/t-coffee/13.39.0-CentOS-vanilla.lua <<'EOD'
-- added manually
prepend_path("PATH", root .. "/bin/linux")
setenv("DIR_4_TCOFFEE",root)
setenv("PLUGINS_4_TCOFFEE",root .. "/plugins/linux")
setenv("TMP_4_TCOFFEE","/tmp/TCOFFEE/tmp")
setenv("LOCKDIR_4_TCOFFEE","/tmp/TCOFFEE/lockdir")
setenv("CACHE_4_TCOFFEE","/tmp/TCOFFEE/cache")
setenv("PDB_DIR","/pdb")
setenv("NO_REMOTE_PDB_DIR","1")
EOD
The contents of /pdb match the download site, that is the top level
consists of
directories which are two letter hashes like "b3" and in those
directories there are
files like "1b30.pdb.gz". It does not have any "unreleased" data
locally.
The intent is to NOT do any local blasts or other searches against that
PDB database, just
to retrieve from it when needed.
Some problem using Expresso like this though:
module load t-coffee
t_coffee -mode expresso -seq /tmp/three.pfa -email
mat...@caltech.edu >three.out 2>&1
the output file "tree.out" contains a very large number of warnings
like:
19541 -- WARNING: PDB_ENTRY_TYPE_FILE must be set to the location of
<pdb>/derived_data/pdb_entry_type.txt when using NO_REMOTE_PDB_DIR=1
19541 -- WARNING: Cannot find pdb_entry_type.txt; 3CHNC is assumed to
be valid; add
ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt in
/tmp/TCOFFE
E/cache/// to automatically check name status
19541 -- WARNING: UNREALEASED_FILE must be set to the location of your
unrealeased.xml file as downloaded from
http://www.rcsb.org/pdb/rest/getUnreleased when
using NO_REMOTE_PDB_DIR=1
19541 -- WARNING: UNREALEASED_FILE must be set to the location of your
unrealeased.xml file as downloaded from
http://www.rcsb.org/pdb/rest/getUnreleased when
using NO_REMOTE_PDB_DIR=1
19541 -- WARNING: Cannot find unrealeased.xml; 3CHNC is assumed to be
released;
Each of the three input sequences also generates a:
>one No Template Selected
message. That is odd because these three are derived from pir:a1hu,
each with tiny modifications. Unmodified pir:a1hu matches perfectly
with Swissprot P01876.2, for which there are PDB structures:
https://www.ncbi.nlm.nih.gov/protein/P01876.2?report=genbank&log$=prottop&blast_rank=1&RID=
So I think something must be configured wrong here. Any idea what that
might be?
The input and output files are attached.
Thanks,
David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech