AQ2X - Converting distance restraints 
-------------------------------------
 
AQ2X - Aqua program directory: /u02/jurgen/src/aqua3.2
 
*
* Processing coordinate file 1xxx_1.pdb into Aqua file
*
===== Welcome to AquaWhat ===== version 3.2
called with arguments: set batch on exec aqua readone 1xxx_1.pdb write tmp quit
Project name: 1xxx_1
   (in StrucsetInit: Initialization of strucset <Set1> completed)
Option <restrinp> (word): <none>
Option <coordinp> (word): <none>
Option <coordout> (word): <aqua>
Option <element_guess_pdb> : <false>
Option <terseness> (integer): <0>
Main menu - choose command from: exec, set, read, readone, quit
<Command read: set>
<Command read: batch>
<Command read: on>
Option <batch> : <true>
<Command read: exec>
<Command read: aqua>
<Command read: set>
<Command read: coordinp>
<Command read: pdb>
Option <coordinp> (word): <pdb>
Main menu - choose command from: exec, set, read, readone, quit
<Command read: set>
<Command read: oldmap>
Ignoring option <oldmap>
<Command read: off>
Main menu - choose command from: exec, set, read, readone, quit
<Command read: set>
<Command read: restrinp>
<Command read: diana>
Option <restrinp> (word): <diana>
Main menu - choose command from: exec, set, read, readone, quit
<Command read: set>
<Command read: multiple>
Ignoring option <multiple>
<Command read: off>
Main menu - choose command from: exec, set, read, readone, quit
<Command read: readone>
   (in ReadMenu: starting to read strucset <Set1>)
   (in ReadMenu: using the routines from AquaFuncts_io.c)
<Command read: 1xxx_1.pdb>
Will read 1677 atoms from each file

Next file <1xxx_1.pdb>:
   (in Alloc_cv: memory allocated)
Warning - rewinding the input file before reading next structure
structure 1 read
   (in ToAqua_cv: allocating new molecule)
   (in FillAtoms_cv: allocating 1677 atoms in new molecule)
   (in MakeResidues: allocating 102 residues in molecule of strucset <Set1>)
   (in ToAqua_cv: allocating new structure)
   (in FillCoords_cv: allocating coordinates in new structure)

Read 1 structure(s) from file <1xxx_1.pdb>
   (in Free_cv: memory freed)

The set <Set1> now contains 1 structure(s)
   (in MapAtomsInSet: preparing to map atom names in strucset <Set1>)
Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-pdb
   (in ProcessAtomLIB: reading standard AtomLIB)
   (in ProcessAtomLIB: 982 atom name definitions read)
   (in MapAtomsInMol: mapping external to internal atom names)
   (in MapAtomsInMol: using routine FindAtom3)
 External atom name not found: (1) MET 1 HT1
copying atom name instead
 External atom name not found: (1) MET 1 HT2
copying atom name instead
 External atom name not found: (1) MET 1 HT3
copying atom name instead
 External atom name not found: (102) CYS 102 OT1
copying atom name instead
 External atom name not found: (102) CYS 102 OT2
copying atom name instead
 * One or more atoms could not be found in the AtomLIB
<Command read: write>
   (in WriteMenu: starting to write strucset <Set1>)
<Command read: tmp>
Now opening: 1xxx_1_orig_tmp.set
1 structure has been written
 * Number of structures: 1
 * Number of residues:   102
 * Number of atoms:      1677
<Command read: quit>
*
* Processing restraint file temp.all
*
===== Welcome to AquaHow ===== version 3.2
called with arguments: set batch on exec aqua mol orig tmp noe aqua temp.all out xplor 1xxx_noe.temp ' Converted from temp.all (AQUA version 3.2)' quit
Project name: 1xxx_1
   (in StrucsetInit: Initialization of strucset <theSet> completed)
Option <restrinp> (word): <none>
Option <skip> : <true>
Option <guess> : <true>
Option <multiple> : <true>
Option <sort> (word): <none>
Option <terseness> (integer): <0>
Main menu - choose command from: exec, set, sets, readinf, mol, quit
<Command read: set>
<Command read: batch>
<Command read: on>
Option <batch> : <true>
<Command read: exec>
<Command read: aqua>
<Command read: set>
<Command read: coordinp>
Ignoring option <coordinp>
<Command read: pdb>
Main menu - choose command from: exec, set, sets, readinf, mol, quit
<Command read: set>
<Command read: oldmap>
<Command read: off>
Option <oldmap> : <false>
Main menu - choose command from: exec, set, sets, readinf, mol, quit
<Command read: set>
<Command read: restrinp>
<Command read: diana>
Option <restrinp> (word): <diana>
Main menu - choose command from: exec, set, sets, readinf, mol, quit
<Command read: set>
<Command read: multiple>
<Command read: off>
Option <multiple> : <false>
Main menu - choose command from: exec, set, sets, readinf, mol, quit
<Command read: mol>
<Command read: orig>
<Command read: tmp>
Now opening: 1xxx_1_orig_tmp.set
   (in MakeResidues: allocating 102 residues in molecule of strucset <theSet>)
A molecule has been read
Coordinate set 1 has been read
1 Coordinate set has been read
<Command read: noe>
   (in ProcessDRInput: Beginning restraint input)
<Command read: aqua>
<Command read: temp.all>
Restraint-file <temp.all> opened for reading in <Aqua simple restraint> format
Will read 1242 restraints
   (in ReadRestraintFile: expecting restraints of type NOE)
 * Read 1242 distance restraints successfully!
   (in ProcessDRInput: Restraint input finished)
   (in MapDRInput: mapping atom names)
   (in MapAtomsInDRestraints: preparing to map atom names in the restraint list)
Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-diana
   (in ProcessAtomLIB: reading standard AtomLIB)
   (in ProcessAtomLIB: 489 atom name definitions read)
   (in MapAtomsIn1DR: mapping external to internal atom names)
   (in MapAtomsIn1DR: using routine FindAtom3)
   (in MapAtomsIn1DR: guessing ON)
Option <restrinp> (word): <diana>
<Command read: out>
   (in ProcessDROutput: Beginning restraint output)
<Command read: xplor>
<Command read: 1xxx_noe.temp>
   (in MapAtomsInDRestraints: preparing to map atom names in the restraint list)
Now opening: /u02/jurgen/src/aqua3.2/data/AtomLIB-xplor
   (in ProcessAtomLIB: reading standard AtomLIB)
   (in ProcessAtomLIB: 677 atom name definitions read)
   (in MapAtomsIn1DR: mapping internal to external atom names)
   (in MapAtomsIn1DR: using routine FindAtom3)
   (in MapAtomsIn1DR: guessing OFF)
<Command read: '>
<Command read: Converted>
<Command read: from>
<Command read: temp.all>
<Command read: (AQUA>
<Command read: version>
<Command read: 3.2)'>
 * Distance restraints have been written
   (in ProcessDROutput: Restraint output finished)
<Command read: quit>