updated the documentation

docs/tcoffee_faq.rst

@@ -570,6 +570,7 @@ A: This is true. By default the structures are feteched on the net, using RCSB.
 
 
 
+
 Interestingly, the observation that sequences without structures are those that take the most time to be checked is a reminder of the strongest rational argument that I know of against torture: any innocent would require the maximum amount of torture to establish his/her innocence, which sounds...ahem...strange., and at least inneficient. Then again I was never struck by the efficiency of the Bush administration.
 
 
@@ -623,6 +624,19 @@ You can then edit the script to suit your needs. T-Coffee will use your edited v
 
 If you make extensive modifications, I would appreciate you send me the corrected file so that I can incorporate it in the next distribution.
 
+By default, T-Coffee also requires two important PDB files declared using the two following variables. These variables do not need to be set if the considered files are in the cache directory (default behavior). 
+
+::
+  export PDB_ENTRY_TYPE_FILE=<location of the file pdb_entry_type.txt>
+  Found at: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt
+
+And 
+
+::
+  export PDB_UNREALEASED_FILE=<location of the file unrealeased.xml>
+  Found at: http://www.rcsb.org/pdb/rest/getUnreleased
+
+.. warning:: Since the file unreleased.xml is not part of the pdb distribution, T-Coffee will make an attempt to obtain it even when using the NO_REMOTE_PDB_DIR=1 mode. You must therefore make sure that the file PDB_UNREALEASED_FILE is pointing to is read and write.
 
 Alignment Evaluation
 ====================

docs/tcoffee_manual.rst

@@ -1449,6 +1449,22 @@ If the file you are looking for is neither in the current directory nor in the l
   t_coffee -other_pg extract_from_pdb -infile 1PPGE -fasta -no_remote_pdb_file
 
 
+By default, T-Coffee also requires two important PDB files declared using the two following variables. These variables do not need to be set if the considered files are in the cache directory (default behavior). 
+
+::
+  export PDB_ENTRY_TYPE_FILE=<location of the file pdb_entry_type.txt>
+  Found at: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt
+
+And 
+
+::
+  export PDB_UNREALEASED_FILE=<location of the file unrealeased.xml>
+  Found at: http://www.rcsb.org/pdb/rest/getUnreleased
+
+.. warning:: Since the file unreleased.xml is not part of the pdb distribution, T-Coffee will make an attempt to obtain it even when using the NO_REMOTE_PDB_DIR=1 mode. You must therefore make sure that the file PDB_UNREALEASED_FILE is pointing to is read and write.
+
+
+
 
 ********************************************
 Manipulating RNA sequences with seq_reformat

lib/perl/lib/scripts/extract_from_pdb

@@ -5,6 +5,12 @@ use FileHandle;
 use Cwd;
 use File::Path;
 use Sys::Hostname;
+########################## ENVIRONEMENT VARIABLES ##########
+# PDB_UNREALEASED_FILE
+# PDB_ENTRY_TYPE_FILE
+# NO_REMOTE_PDB_DIR
+# PDB_DIR
+
 ########################## GLOBAL VARIABLES ################
 our $PIDCHILD;
 our $ERROR_DONE;