--- mmdb-1.21.orig/debian/watch
+++ mmdb-1.21/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.ebi.ac.uk/~keb/cldoc/downloads/mmdb-([\d.]*)\.tar\.gz
--- mmdb-1.21.orig/debian/libmmdb0.install
+++ mmdb-1.21/debian/libmmdb0.install
@@ -0,0 +1 @@
+debian/tmp/usr/lib/libmmdb.so.*
--- mmdb-1.21.orig/debian/libmmdb0.symbols
+++ mmdb-1.21/debian/libmmdb0.symbols
@@ -0,0 +1,3674 @@
+libmmdb.so.0 libmmdb0 #MINVER#
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+ _ZTV8CExpData@Base 1.09
+ _ZTV8CJournal@Base 1.09
+ _ZTV8CObsLine@Base 1.09
+ _ZTV8CResidue@Base 1.09
+ _ZTV8CRevData@Base 1.09
+ _ZTV8CSBAngle@Base 1.09
+ _ZTV8CSBIndex@Base 1.09
+ _ZTV9CAtomPath@Base 1.09
+ _ZTV9CCompound@Base 1.09
+ _ZTV9CKeyWords@Base 1.09
+ _ZTV9CMContact@Base 1.09
+ _ZTV9CMMDBFile@Base 1.09
+ _ZTV9CProModel@Base 1.09
+ autoserials_@Base 1.09
+ floatMachEps@Base 1.09
+ hy36decode@Base 1.19
+ hy36encode@Base 1.19
+ ignoreCharge@Base 1.09
+ ignoreElement@Base 1.09
+ ignoreNonCoorPDBErrors@Base 1.09
+ ignoreSegID@Base 1.09
+ ignoreUnmatch@Base 1.09
+ mmCIFData@Base 1.09
+ mmdb_f_advance_@Base 1.09
+ mmdb_f_atom_@Base 1.09
+ mmdb_f_bksp_@Base 1.09
+ mmdb_f_close_@Base 1.09
+ mmdb_f_coord_@Base 1.09
+ mmdb_f_copy_@Base 1.09
+ mmdb_f_copyatom_@Base 1.09
+ mmdb_f_cvanisou_@Base 1.09
+ mmdb_f_delete_@Base 1.09
+ mmdb_f_gethet_@Base 1.09
+ mmdb_f_init_@Base 1.09
+ mmdb_f_open_@Base 1.09
+ mmdb_f_openl_@Base 1.09
+ mmdb_f_orthmat_@Base 1.09
+ mmdb_f_quit_@Base 1.09
+ mmdb_f_rbcell_@Base 1.09
+ mmdb_f_rbcelln_@Base 1.09
+ mmdb_f_rborf_@Base 1.09
+ mmdb_f_rbrcel_@Base 1.09
+ mmdb_f_rbspgrp_@Base 1.09
+ mmdb_f_rewd_@Base 1.09
+ mmdb_f_seek_@Base 1.09
+ mmdb_f_setcell_@Base 1.09
+ mmdb_f_sethet_@Base 1.09
+ mmdb_f_setname_@Base 1.09
+ mmdb_f_setter_@Base 1.09
+ mmdb_f_settype_@Base 1.09
+ mmdb_f_wbcell_@Base 1.09
+ mmdb_f_wbspgrp_@Base 1.09
+ mmdb_f_wremark_@Base 1.09
+ mmdb_f_write_@Base 1.09
+ mmdb_fcif_create_@Base 1.09
+ mmdb_fcif_init_@Base 1.09
+ mmdb_fcif_putdate_@Base 1.09
+ mmdb_fcif_putdot_@Base 1.09
+ mmdb_fcif_putinteger_@Base 1.09
+ mmdb_fcif_putloopdot_@Base 1.09
+ mmdb_fcif_putloopinteger_@Base 1.09
+ mmdb_fcif_putloopquestion_@Base 1.09
+ mmdb_fcif_putloopreal_@Base 1.09
+ mmdb_fcif_putloopstring_@Base 1.09
+ mmdb_fcif_putquestion_@Base 1.09
+ mmdb_fcif_putreal_@Base 1.09
+ mmdb_fcif_putstring_@Base 1.09
+ mmdb_fcif_quit_@Base 1.09
+ mmdb_fcif_write_@Base 1.09
+ rbcheckerr_@Base 1.09
+ rberrstop_@Base 1.09
+ rhombohedral@Base 1.19
+ setreadcoords_@Base 1.09
+ short_mono@Base 1.19
+ simrwbrook_@Base 1.09
+ special@Base 1.19
--- mmdb-1.21.orig/debian/changelog
+++ mmdb-1.21/debian/changelog
@@ -0,0 +1,28 @@
+mmdb (1.21-0ubuntu2) lucid; urgency=low
+
+  * Incorporate patches from ccp4 version 6.1.3
+
+ -- Morten Kjeldgaard <mok0@ubuntu.com>  Tue, 26 Jan 2010 18:02:32 +0100
+
+mmdb (1.21-0ubuntu1) karmic; urgency=low
+
+  * New upstream version.
+
+ -- Morten Kjeldgaard <mok0@ubuntu.com>  Tue, 16 Jun 2009 12:48:36 +0200
+
+mmdb (1.19-0ubuntu1) jaunty; urgency=low
+
+  * New upstream version.
+  * Add libmmdb0.symbols file for minimal dependency checking.
+  * Patched various minor compilation warnings.
+  * debian/control: bump standards-version to current (3.8.0)
+    Include dependency on quilt & autotools-dev (so cdbs can copy 
+    config.guess and config.sub)
+
+ -- Morten Kjeldgaard <mok0@ubuntu.com>  Tue, 10 Feb 2009 11:56:44 +0100
+
+mmdb (1.09.1-0ubuntu1) hardy; urgency=low
+
+  * Initial packaging (LP: #176218)
+	
+ -- Morten Kjeldgaard <mok@bioxray.au.dk>  Fri, 11 Jan 2008 17:42:16 +0100
--- mmdb-1.21.orig/debian/mmdb.pc
+++ mmdb-1.21/debian/mmdb.pc
@@ -0,0 +1,12 @@
+prefix=/usr
+exec_prefix=/usr
+libdir=/usr/lib
+includedir=/usr/include
+
+Name: mmdb
+Description: Macromolecular coordinate library
+Version: 1.19
+Requires:
+Conflicts:
+Libs: -L${libdir} -lmmdb
+Cflags: -I${includedir}
--- mmdb-1.21.orig/debian/libmmdb0.docs
+++ mmdb-1.21/debian/libmmdb0.docs
@@ -0,0 +1 @@
+README
--- mmdb-1.21.orig/debian/compat
+++ mmdb-1.21/debian/compat
@@ -0,0 +1 @@
+5
--- mmdb-1.21.orig/debian/control
+++ mmdb-1.21/debian/control
@@ -0,0 +1,49 @@
+Source: mmdb
+Priority: optional
+Maintainer: Morten Kjeldgaard <mok0@ubuntu.com>
+Homepage: http://www.ebi.ac.uk/~keb/cldoc/downloads/
+Build-Depends: debhelper (>= 5), cdbs, autotools-dev, quilt
+Standards-Version: 3.8.3
+Section: science
+
+Package: libmmdb-dev
+Section: libdevel
+Architecture: any
+Depends: libmmdb0 (=  ${binary:Version} ), ${misc:Depends}
+Description: macromolecular coordinate library developer files
+ MMDB, written by Eugene Krissinel of the EBI, is designed to assist
+ developers in working with macromolecular coordinate files. The
+ library handles both PDB and mmCIF format files.
+ .
+ The Library also features an internal binary format, portable between
+ different platforms. This is achieved at uniformity of the Library's
+ interface functions, so that there is no difference in handling different
+ formats.
+ .
+ MMDB provides various high-level tools for working with coordinate files,
+ including reading and writing, orthogonal-fractional transforms,
+ generation of symmetry mates, editing the molecular structure and more.
+ .
+ This package contains library and header files needed for program
+ development.
+
+Package: libmmdb0
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: macromolecular coordinate library
+ MMDB, written by Eugene Krissinel of the EBI, is designed to assist
+ developers in working with macromolecular coordinate files. The
+ library handles both PDB and mmCIF format files.
+ .
+ The Library also features an internal binary format, portable between
+ different platforms. This is achieved at uniformity of the Library's
+ interface functions, so that there is no difference in handling different
+ formats.
+ .
+ MMDB provides various high-level tools for working with coordinate files,
+ including reading and writing, orthogonal-fractional transforms,
+ generation of symmetry mates, editing the molecular structure and more.
+ .
+ This package contains the shared library components needed for programs
+ that have been linked to the mmdb library.
--- mmdb-1.21.orig/debian/README.source
+++ mmdb-1.21/debian/README.source
@@ -0,0 +1,57 @@
+This package uses quilt to manage all modifications to the upstream
+source.  Changes are stored in the source package as diffs in
+debian/patches and applied during the build.
+
+To configure quilt to use debian/patches instead of patches, you want
+either to export QUILT_PATCHES=debian/patches in your environment
+or use this snippet in your ~/.quiltrc:
+
+    for where in ./ ../ ../../ ../../../ ../../../../ ../../../../../; do
+        if [ -e ${where}debian/rules -a -d ${where}debian/patches ]; then
+                export QUILT_PATCHES=debian/patches
+        fi
+    done
+
+To get the fully patched source after unpacking the source package, cd to
+the root level of the source package and run:
+
+    quilt push -a
+
+The last patch listed in debian/patches/series will become the current
+patch.
+
+To add a new set of changes, first run quilt push -a, and then run:
+
+    quilt new <patch>
+
+where <patch> is a descriptive name for the patch, used as the filename in
+debian/patches.  Then, for every file that will be modified by this patch,
+run:
+
+    quilt add <file>
+
+before editing those files.  You must tell quilt with quilt add what files
+will be part of the patch before making changes or quilt will not work
+properly.  After editing the files, run:
+
+    quilt refresh
+
+to save the results as a patch.
+
+Alternately, if you already have an external patch and you just want to
+add it to the build system, run quilt push -a and then:
+
+    quilt import -P <patch> /path/to/patch
+    quilt push -a
+
+(add -p 0 to quilt import if needed). <patch> as above is the filename to
+use in debian/patches.  The last quilt push -a will apply the patch to
+make sure it works properly.
+
+To remove an existing patch from the list of patches that will be applied,
+run:
+
+    quilt delete <patch>
+
+You may need to run quilt pop -a to unapply patches first before running
+this command.
--- mmdb-1.21.orig/debian/libmmdb-dev.install
+++ mmdb-1.21/debian/libmmdb-dev.install
@@ -0,0 +1,4 @@
+debian/tmp/usr/include/mmdb/*
+debian/tmp/usr/lib/libmmdb.a
+debian/tmp/usr/lib/libmmdb.so
+debian/mmdb.pc /usr/lib/pkgconfig
--- mmdb-1.21.orig/debian/copyright
+++ mmdb-1.21/debian/copyright
@@ -0,0 +1,56 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Upstream-Name: mmdb
+Upstream-Maintainer: Eugene Krissinel <keb@ebi.ac.uk>
+Upstream-Source: http://www.ebi.ac.uk/~keb/cldoc/downloads/
+
+Files: src/*, Examples/*
+Copyright: © 2004, Eugene Krissinel
+License: LGPL-2.1
+ This library is free software and is distributed under the terms
+ and conditions of the CCP4 licence agreement as `Part 0' (Annex 2)
+ software, which is version 2.1 of the GNU Lesser General Public
+ Licence (LGPL) with the following additional clause:
+ .
+   `You may also combine or link a "work that uses the Library"
+    to produce a work containing portions of the Library, and
+    distribute that work under terms of your choice, provided that
+    you give prominent notice with each copy of the work that the
+    specified version of the Library is used in it, and that you
+    include or provide public access to the complete corresponding
+    machine-readable source code for the Library including whatever
+    changes were used in the work. (i.e. If you make changes to the
+    Library you must distribute those, but you do not need to
+    distribute source or object code to those portions of the work
+    not covered by this licence.)'
+ .
+ Note that this clause grants an additional right and does not
+ impose any additional restriction, and so does not affect
+ compatibility with the GNU General Public Licence (GPL). If you
+ wish to negotiate other terms, please contact the maintainer.
+ .
+ You can redistribute it and/or modify the library under the terms
+ of the GNU Lesser General Public License as published by the Free
+ Software Foundation; either version 2.1 of the License, or (at
+ your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the CCP4 licence and/or GNU
+ Lesser General Public License along with this library; if not,
+ write to the CCP4 Secretary, Daresbury Laboratory, Warrington
+ WA4 4AD, UK.
+
+X-Comment: On Debian systems, the complete text of the GNU Lesser
+ General Public License version 2.1 can be found in the file
+ /usr/share/common-licenses/LGPL-2.1.
+
+Files: hybrid_36.*
+Copyright: © 2007, Ralf W. Grosse-Kunstleve
+License: Unrestricted Open Source (cctbx.sf.net).
+
+Files: debian/*, configure.ac, */Makefile.am
+Copyright: © 2007-2009, Morten Kjeldgaard <mok@bioxray.au.dk>
+License: LGPL-2.1
--- mmdb-1.21.orig/debian/rules
+++ mmdb-1.21/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+
+CXXFLAGS += -D_REENTRANT
--- mmdb-1.21.orig/debian/patches/series
+++ mmdb-1.21/debian/patches/series
@@ -0,0 +1,7 @@
+06-mmdb_coormngr.cpp
+05-linalg_.cpp
+04-file_.cpp
+03-mmdb_sbase0.cpp
+02-bfsg_min.cpp
+01-mmdb_rwbrook.cpp
+ccp4-6.1.3.patch
--- mmdb-1.21.orig/debian/patches/01-mmdb_rwbrook.cpp
+++ mmdb-1.21/debian/patches/01-mmdb_rwbrook.cpp
@@ -0,0 +1,19 @@
+--- mmdb.orig/src/mmdb_rwbrook.cpp
++++ mmdb/src/mmdb_rwbrook.cpp
+@@ -1469,7 +1469,7 @@
+             fpstr ID,     int   ID_len,
+             int * iRet
+            ) )  {
+-int      k,i,RC;
++int      k, RC;
+ ChainID  chainID;
+ ResName  resName;
+ InsCode  insCode;
+@@ -1478,7 +1478,6 @@
+ SegID    sgID;
+ Element  element;
+ PCAtom   atom;
+-pstr     p;
+ char     charge[10];
+ 
+   strcpy ( LastFunc,"MMDB_F_Atom" );
--- mmdb-1.21.orig/debian/patches/06-mmdb_coormngr.cpp
+++ mmdb-1.21/debian/patches/06-mmdb_coormngr.cpp
@@ -0,0 +1,30 @@
+--- mmdb.orig/src/mmdb_coormngr.cpp
++++ mmdb/src/mmdb_coormngr.cpp
+@@ -834,7 +834,7 @@
+ void CMMDBCoorManager::SwapModels ( int modelNo1, int modelNo2 )  {
+ PCModel model;
+ PPCAtom A;
+-int     m1,m2,i11,i12,i21,i22,i,k,n;
++int     m1,m2,i11,i12,i21,i22,i,k, n = 0;
+ 
+   m1 = IMax ( 0,modelNo1-1 );
+   m2 = IMin ( nModels,modelNo2) - 1;
+@@ -3168,6 +3168,8 @@
+ int       nAtoms;
+ int       i,j,k,n,m,nt, ic,jc,kc, is,js,ks;
+ 
++ is = js = ks = 0;
++
+   if (!Cryst.areMatrices())  return -1;
+ 
+   Cryst.Frac2Orth ( 0.5,0.5,0.5, x0,y0,z0 );
+@@ -3291,6 +3293,9 @@
+ int       i1;
+ Boolean   B0,B;
+ 
++ x0 = y0 = z0 = 0.0;
++ x = y = z = 0.0;
++
+   res = atom->residue;
+   if ((!res) || (seqDist<=0))  {
+     seq1 = MaxInt4;
--- mmdb-1.21.orig/debian/patches/ccp4-6.1.3.patch
+++ mmdb-1.21/debian/patches/ccp4-6.1.3.patch
@@ -0,0 +1,673 @@
+--- mmdb.orig/src/bfgs_min.cpp
++++ mmdb/src/bfgs_min.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: bfgs_min.cpp,v 1.5 2008/07/08 15:28:14 keb Exp $
++//  $Id: bfgs_min.cpp,v 1.14 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/bfgs_min.h
++++ mmdb/src/bfgs_min.h
+@@ -1,4 +1,4 @@
+-//  $Id: bfgs_min.h,v 1.7 2008/07/08 15:28:14 keb Exp $
++//  $Id: bfgs_min.h,v 1.15 2008/08/21 09:54:01 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/file_.cpp
++++ mmdb/src/file_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: file_.cpp,v 1.19 2008/07/08 15:28:14 keb Exp $
++//  $Id: file_.cpp,v 1.20.2.2 2009/07/01 10:58:09 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -347,10 +347,10 @@
+           if (i>0)  sleep ( 1 );
+ #endif
+           if (TextMode)  {
+-            if (ReadOnly)  hFile = fopen ( FName,"r"   );
++            if (ReadOnly)  hFile = fopen ( FName,"rt"   );
+                      else  hFile = fopen ( FName,"r+t" );
+           } else  {
+-            if (ReadOnly)  hFile = fopen ( FName,"r"   );
++            if (ReadOnly)  hFile = fopen ( FName,"rb"   );
+                      else  hFile = fopen ( FName,"r+b" );
+           }
+ #ifndef _MVS
+--- mmdb.orig/src/file_.h
++++ mmdb/src/file_.h
+@@ -1,4 +1,4 @@
+-//  $Id: file_.h,v 1.15 2008/07/08 15:28:14 keb Exp $
++//  $Id: file_.h,v 1.17 2008/08/21 09:54:01 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/linalg_.cpp
++++ mmdb/src/linalg_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: linalg_.cpp,v 1.8 2008/07/08 15:28:14 keb Exp $
++//  $Id: linalg_.cpp,v 1.15 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/linalg_.h
++++ mmdb/src/linalg_.h
+@@ -1,4 +1,4 @@
+-//  $Id: linalg_.h,v 1.9 2008/07/08 15:28:14 keb Exp $
++//  $Id: linalg_.h,v 1.15 2008/08/21 09:54:01 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/machine_.cpp
++++ mmdb/src/machine_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: machine_.cpp,v 1.5 2008/07/08 15:28:14 keb Exp $
++//  $Id: machine_.cpp,v 1.15 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/machine_.h
++++ mmdb/src/machine_.h
+@@ -1,4 +1,4 @@
+-//  $Id: machine_.h,v 1.6 2008/07/08 15:28:14 keb Exp $
++//  $Id: machine_.h,v 1.24 2008/09/03 08:51:26 FR45 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -127,8 +127,12 @@
+ # define CALL_LIKE_VMS  1
+ 
+ // MVS stands for Microsoft Visual Studio
+-#elif defined(_MVS) 
++#elif defined(_MSC_VER)
++# if (_MSC_VER) >= 800
++# define CALL_LIKE_MVS  2
++# else
+ # define CALL_LIKE_MVS  1
++# endif
+ 
+ #elif defined(F2C) || defined(G77)
+ # define CALL_LIKE_SUN  8
+@@ -400,6 +404,36 @@
+ 
+ #elif defined(CALL_LIKE_MVS)
+ 
++# if ( CALL_LIKE_MVS == 2 )
++
++  typedef pstr fpstr;
++
++# define FTN_STR(s)  s
++# define FTN_LEN(s)  s##_len
++
++# define char_struct(s)           \
++    pstr  s;                      \
++    int   s##_len;
++# define fill_char_struct(s,str)  \
++    s  = str;                     \
++    s##_len = strlen(str);
++
++# ifdef __cplusplus
++#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
++    extern "C" void NAME p_sun
++# else
++#   define FORTRAN_SUBR(NAME,name,p_sun,p_stardent,p_mvs) \
++    void NAME p_sun
++# endif
++
++# define FORTRAN_EXTERN(NAME,name,p_sun,p_stardent,p_mvs) \
++    extern "C" void NAME p_sun
++
++# define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
++    NAME p_sun
++
++# else
++
+   typedef pstr fpstr;
+ 
+ # define FTN_STR(s)  s
+@@ -425,7 +459,7 @@
+ 
+ # define FORTRAN_CALL(NAME,name,p_sun,p_stardent,p_mvs) \
+     NAME p_mvs
+-
++# endif
+ #else
+ 
+ # error  Unknown machine!!!
+--- mmdb.orig/src/math_.cpp
++++ mmdb/src/math_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: math_.cpp,v 1.6 2008/07/08 15:28:14 keb Exp $
++//  $Id: math_.cpp,v 1.14 2008/08/21 09:54:06 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/math_.h
++++ mmdb/src/math_.h
+@@ -1,4 +1,4 @@
+-//  $Id: math_.h,v 1.6 2008/07/08 15:28:14 keb Exp $
++//  $Id: math_.h,v 1.14 2008/08/21 09:54:01 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mattype_.cpp
++++ mmdb/src/mattype_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mattype_.cpp,v 1.12 2008/07/08 15:28:14 keb Exp $
++//  $Id: mattype_.cpp,v 1.20.2.2 2009/09/28 13:43:33 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mattype_.h
++++ mmdb/src/mattype_.h
+@@ -1,4 +1,4 @@
+-//  $Id: mattype_.h,v 1.11 2008/07/08 15:28:15 keb Exp $
++//  $Id: mattype_.h,v 1.19.2.2 2009/09/28 13:43:34 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_align.cpp
++++ mmdb/src/mmdb_align.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_align.cpp,v 1.10 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_align.cpp,v 1.16 2008/08/21 09:54:06 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_align.h
++++ mmdb/src/mmdb_align.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_align.h,v 1.7 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_align.h,v 1.15 2008/08/21 09:54:01 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_atom.cpp
++++ mmdb/src/mmdb_atom.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_atom.cpp,v 1.25 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_atom.cpp,v 1.23.2.2 2009/09/28 11:00:25 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_atom.h
++++ mmdb/src/mmdb_atom.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_atom.h,v 1.17 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_atom.h,v 1.22.2.2 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -290,7 +290,7 @@
+     void  CalcAtomStatistics ( RSAtomStat AS );
+     realtype GetDist2 ( PCAtom a );
+     realtype GetDist2 ( PCAtom a, mat44 & tm );  // tm applies to A
+-    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );// tm applies to A
++    realtype GetDist2 ( PCAtom a, mat33 & r, vect3 & t );  // tm applies to A
+     realtype GetDist2 ( realtype ax, realtype ay, realtype az );
+ 
+     // GetCosine(a1,a2) calculates cosine of angle a1-this-a2,
+--- mmdb.orig/src/mmdb_bondmngr.cpp
++++ mmdb/src/mmdb_bondmngr.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_bondmngr.cpp,v 1.7 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_bondmngr.cpp,v 1.14 2008/08/21 09:54:06 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_bondmngr.h
++++ mmdb/src/mmdb_bondmngr.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_bondmngr.h,v 1.5 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_bondmngr.h,v 1.14 2008/08/21 09:54:02 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_chain.cpp
++++ mmdb/src/mmdb_chain.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_chain.cpp,v 1.16 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_chain.cpp,v 1.18.2.1 2009/08/21 13:35:09 rmk65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -672,7 +672,8 @@
+     i  = 0;
+     sN = 1;
+     while (i<numRes)  {
+-      PutInteger ( &(S[8]),sN,2 );
++      //PutInteger ( &(S[8]),sN,2 );
++      PutInteger ( &(S[7]),sN,3 );
+       k = 19;
+       while ((i<numRes) && (k<70))  {
+         if (resName[i][0])
+--- mmdb.orig/src/mmdb_chain.h
++++ mmdb/src/mmdb_chain.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_chain.h,v 1.12 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_chain.h,v 1.16 2008/08/21 09:54:02 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_cifdefs.cpp
++++ mmdb/src/mmdb_cifdefs.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_cifdefs.cpp,v 1.5 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_cifdefs.cpp,v 1.14 2008/08/21 09:54:07 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_cifdefs.h
++++ mmdb/src/mmdb_cifdefs.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_cifdefs.h,v 1.6 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_cifdefs.h,v 1.15 2008/08/21 09:54:02 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_coormngr.cpp
++++ mmdb/src/mmdb_coormngr.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_coormngr.cpp,v 1.24 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_coormngr.cpp,v 1.21.2.2 2009/09/28 13:43:34 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_coormngr.h
++++ mmdb/src/mmdb_coormngr.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_coormngr.h,v 1.18 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_coormngr.h,v 1.21.2.2 2009/09/28 13:43:34 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_cryst.cpp
++++ mmdb/src/mmdb_cryst.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_cryst.cpp,v 1.24 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_cryst.cpp,v 1.20 2008/08/21 09:54:07 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_cryst.h
++++ mmdb/src/mmdb_cryst.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_cryst.h,v 1.18 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_cryst.h,v 1.19 2008/08/21 09:54:02 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_defs.h
++++ mmdb/src/mmdb_defs.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_defs.h,v 1.12 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_defs.h,v 1.19.2.2 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_ficif.cpp
++++ mmdb/src/mmdb_ficif.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_ficif.cpp,v 1.6 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_ficif.cpp,v 1.14 2008/08/21 09:54:07 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_ficif.h
++++ mmdb/src/mmdb_ficif.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_ficif.h,v 1.5 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_ficif.h,v 1.14 2008/08/21 09:54:02 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_file.cpp
++++ mmdb/src/mmdb_file.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_file.cpp,v 1.31 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_file.cpp,v 1.25.2.1 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_file.h
++++ mmdb/src/mmdb_file.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_file.h,v 1.24 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_file.h,v 1.22.2.1 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_graph.cpp
++++ mmdb/src/mmdb_graph.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_graph.cpp,v 1.18 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_graph.cpp,v 1.19 2008/08/21 09:54:07 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_graph.h
++++ mmdb/src/mmdb_graph.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_graph.h,v 1.14 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_graph.h,v 1.17 2008/08/21 09:54:03 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_manager.cpp
++++ mmdb/src/mmdb_manager.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_manager.cpp,v 1.10 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_manager.cpp,v 1.17.2.3 2009/09/28 13:43:35 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_manager.h
++++ mmdb/src/mmdb_manager.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_manager.h,v 1.7 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_manager.h,v 1.16.2.3 2009/09/28 13:43:35 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_mask.cpp
++++ mmdb/src/mmdb_mask.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_mask.cpp,v 1.6 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_mask.cpp,v 1.14 2008/08/21 09:54:08 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_mask.h
++++ mmdb/src/mmdb_mask.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_mask.h,v 1.5 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_mask.h,v 1.14 2008/08/21 09:54:03 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_mmcif.cpp
++++ mmdb/src/mmdb_mmcif.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_mmcif.cpp,v 1.11 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_mmcif.cpp,v 1.16.2.1 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_mmcif.h
++++ mmdb/src/mmdb_mmcif.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_mmcif.h,v 1.9 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_mmcif.h,v 1.15.2.1 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_model.cpp
++++ mmdb/src/mmdb_model.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_model.cpp,v 1.19 2008/07/08 15:28:15 keb Exp $
++//  $Id: mmdb_model.cpp,v 1.19.2.1 2008/11/13 09:31:35 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_model.h
++++ mmdb/src/mmdb_model.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_model.h,v 1.12 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_model.h,v 1.18 2008/08/21 09:54:03 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_rwbrook.cpp
++++ mmdb/src/mmdb_rwbrook.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_rwbrook.cpp,v 1.16 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_rwbrook.cpp,v 1.38.2.1 2008/11/27 14:14:25 mdw Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -1469,7 +1469,7 @@
+             fpstr ID,     int   ID_len,
+             int * iRet
+            ) )  {
+-int      k, RC;
++int      k,i,RC;
+ ChainID  chainID;
+ ResName  resName;
+ InsCode  insCode;
+@@ -1551,10 +1551,9 @@
+     } else
+       charge [0] = char(0);
+ 
+-/*
+     if (FTN_STR(ID)[0]==' ')  {
+       atomName[0] = char(0);
+-      if ((FTN_STR(AtNam)[1]=='H') ||
++      if ((FTN_STR(AtNam)[1]=='H') && (FTN_STR(AtNam)[0]!='H') ||
+           ((FTN_STR(AtNam)[1]=='D') && (FTN_STR(ID)[2]=='D')))  {
+         i = 0;
+         while ((i<nHydAtomNames) && 
+@@ -1562,12 +1561,16 @@
+         if (i<nHydAtomNames)
+           GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
+       }
+-      if (!atomName[0])  {
++
++      if ((FTN_STR(AtNam)[0]=='A') || ((FTN_STR(AtNam)[0]=='N') && (FTN_STR(ID)[1]!='N'))) {
++        GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
++      } else if ((FTN_STR(ID)[1]=='N') && ( (FTN_STR(AtNam)[0]=='N') && (FTN_STR(AtNam)[1]=='N') )) {
++        GetStrTer ( atomName,FTN_STR(AtNam),4,5,FTN_LEN(AtNam) );
++      } else if (!atomName[0])  {
+         atomName[0] = ' ';
+         GetStrTer ( &(atomName[1]),FTN_STR(AtNam),3,4,FTN_LEN(AtNam) );
+       }
+     } else
+-*/
+       GetStrTer ( atomName,FTN_STR(AtNam),4,5,4 );
+ 
+ 
+--- mmdb.orig/src/mmdb_rwbrook.h
++++ mmdb/src/mmdb_rwbrook.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_rwbrook.h,v 1.5 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_rwbrook.h,v 1.14 2008/08/21 09:54:03 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_sbase.cpp
++++ mmdb/src/mmdb_sbase.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_sbase.cpp,v 1.12 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_sbase.cpp,v 1.17 2008/08/21 09:54:09 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_sbase.h
++++ mmdb/src/mmdb_sbase.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_sbase.h,v 1.10 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_sbase.h,v 1.16 2008/08/21 09:54:04 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_sbase0.cpp
++++ mmdb/src/mmdb_sbase0.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_sbase0.cpp,v 1.8 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_sbase0.cpp,v 1.12.2.1 2009/07/01 10:52:19 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -1320,7 +1320,11 @@
+     dirpath = new char[i+10];
+     strcpy ( dirpath,path );
+     if (i>0)  {
++#if defined(_MSC_VER) || defined (WIN32)
++      if (dirpath[i-1]!='\\')  strcat ( dirpath,"\\" );
++#else
+       if (dirpath[i-1]!='/')  strcat ( dirpath,"/" );
++#endif
+     }
+   }
+ 
+--- mmdb.orig/src/mmdb_sbase0.h
++++ mmdb/src/mmdb_sbase0.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_sbase0.h,v 1.6 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_sbase0.h,v 1.10.2.1 2009/01/27 11:58:42 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_selmngr.cpp
++++ mmdb/src/mmdb_selmngr.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_selmngr.cpp,v 1.26 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_selmngr.cpp,v 1.18.2.2 2009/07/01 10:53:24 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+@@ -1158,7 +1158,7 @@
+              int   selKey    // selection key
+                     )  {
+ int       i,j,k,n,m1,m2,c, sk,nsel;
+-Boolean   noRes,modelSel,chainSel,resSel,selAND;
++Boolean   noRes,modelSel(False),chainSel,resSel,selAND;
+ PCModel   model;
+ PCChain   chain;
+ PCResidue res;
+--- mmdb.orig/src/mmdb_selmngr.h
++++ mmdb/src/mmdb_selmngr.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_selmngr.h,v 1.15 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_selmngr.h,v 1.16.2.1 2009/01/27 12:01:48 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_symop.cpp
++++ mmdb/src/mmdb_symop.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_symop.cpp,v 1.14 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_symop.cpp,v 1.18 2008/08/21 09:54:09 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_symop.h
++++ mmdb/src/mmdb_symop.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_symop.h,v 1.11 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_symop.h,v 1.16 2008/08/21 09:54:04 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_tables.cpp
++++ mmdb/src/mmdb_tables.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_tables.cpp,v 1.15 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_tables.cpp,v 1.19.2.1 2009/09/28 11:00:26 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_tables.h
++++ mmdb/src/mmdb_tables.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_tables.h,v 1.14 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_tables.h,v 1.19.2.1 2009/09/28 11:00:27 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_title.cpp
++++ mmdb/src/mmdb_title.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_title.cpp,v 1.10 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_title.cpp,v 1.16.2.2 2009/09/28 13:43:35 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_title.h
++++ mmdb/src/mmdb_title.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_title.h,v 1.8 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_title.h,v 1.15.2.1 2009/09/28 11:00:27 ccb Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_uddata.cpp
++++ mmdb/src/mmdb_uddata.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_uddata.cpp,v 1.9 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_uddata.cpp,v 1.14 2008/08/21 09:54:10 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_uddata.h
++++ mmdb/src/mmdb_uddata.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_uddata.h,v 1.6 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_uddata.h,v 1.14 2008/08/21 09:54:04 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_utils.cpp
++++ mmdb/src/mmdb_utils.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_utils.cpp,v 1.25 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_utils.cpp,v 1.26 2008/08/21 09:54:10 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_utils.h
++++ mmdb/src/mmdb_utils.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_utils.h,v 1.16 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_utils.h,v 1.19 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_xml.cpp
++++ mmdb/src/mmdb_xml.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_xml.cpp,v 1.11 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_xml.cpp,v 1.19 2008/08/21 09:54:10 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/mmdb_xml.h
++++ mmdb/src/mmdb_xml.h
+@@ -1,4 +1,4 @@
+-//  $Id: mmdb_xml.h,v 1.6 2008/07/08 15:28:16 keb Exp $
++//  $Id: mmdb_xml.h,v 1.15 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/random_n.cpp
++++ mmdb/src/random_n.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: random_n.cpp,v 1.6 2008/07/08 15:28:16 keb Exp $
++//  $Id: random_n.cpp,v 1.14 2008/08/21 09:54:10 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/random_n.h
++++ mmdb/src/random_n.h
+@@ -1,4 +1,4 @@
+-//  $Id: random_n.h,v 1.6 2008/07/08 15:28:16 keb Exp $
++//  $Id: random_n.h,v 1.14 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/stream_.cpp
++++ mmdb/src/stream_.cpp
+@@ -1,4 +1,4 @@
+-//  $Id: stream_.cpp,v 1.5 2008/07/08 15:28:16 keb Exp $
++//  $Id: stream_.cpp,v 1.14 2008/08/21 09:54:10 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
+--- mmdb.orig/src/stream_.h
++++ mmdb/src/stream_.h
+@@ -1,4 +1,4 @@
+-//  $Id: stream_.h,v 1.5 2008/07/08 15:28:16 keb Exp $
++//  $Id: stream_.h,v 1.14 2008/08/21 09:54:05 nds65 Exp $
+ //  =================================================================
+ //
+ //   CCP4 Coordinate Library: support of coordinate-related
--- mmdb-1.21.orig/debian/patches/02-bfsg_min.cpp
+++ mmdb-1.21/debian/patches/02-bfsg_min.cpp
@@ -0,0 +1,11 @@
+--- mmdb.orig/src/bfgs_min.cpp
++++ mmdb/src/bfgs_min.cpp
+@@ -621,6 +621,8 @@
+ realtype Lambda,LamTem, LamPre, FplPre, A, B;
+ realtype Disc,  B1, B2, Lambda0;
+ 
++ LamPre = FplPre = 0.0;  // to avoid them being undefined when
++                         // computing B1 and B2
+   MaxTkn  = False;
+   RetCode = 2;
+   Alpha   = 1.0e-4;
--- mmdb-1.21.orig/debian/patches/03-mmdb_sbase0.cpp
+++ mmdb-1.21/debian/patches/03-mmdb_sbase0.cpp
@@ -0,0 +1,20 @@
+--- mmdb.orig/src/mmdb_sbase0.cpp
++++ mmdb/src/mmdb_sbase0.cpp
+@@ -738,7 +738,7 @@
+ // superposes exactly the atoms A1[0] and A2[0].
+ realtype det,B;
+ vect3    vc1,vc2;
+-int      i,j,k,i1,i2;
++ int      i,j,k;
+ 
+   //  1.  Calculate the correlation matrix. The rotation will be
+   //      done around
+@@ -1484,7 +1484,7 @@
+ 
+ 
+ int CSBase0::GetStructNo ( cpstr compoundID )  {
+-int  l1,l2,l,k;
++int  l1,l2, l=0, k=0;
+ char id[20];
+   strcpy_css ( id,compoundID );
+   l1 = 0;
--- mmdb-1.21.orig/debian/patches/05-linalg_.cpp
+++ mmdb-1.21/debian/patches/05-linalg_.cpp
@@ -0,0 +1,11 @@
+--- mmdb.orig/src/linalg_.cpp
++++ mmdb/src/linalg_.cpp
+@@ -575,7 +575,7 @@
+ //
+ //
+ int       ItnLimit=300;
+-int       i,j,k,l,i1,k1,l1,its,mn,ExitKey;
++int       i,j,k,l,i1,k1,l1=0,its,mn,ExitKey;
+ realtype  C,G,F,X,S,H,Y,Z,Scale,ANorm,GG;
+ 
+   RetCode = 0;
--- mmdb-1.21.orig/debian/patches/04-file_.cpp
+++ mmdb-1.21/debian/patches/04-file_.cpp
@@ -0,0 +1,40 @@
+--- mmdb.orig/src/file_.cpp
++++ mmdb/src/file_.cpp
+@@ -76,7 +76,7 @@
+ // ===================  Auxilary Functions  =========================
+ 
+ pstr GetFPath ( pstr FilePath, int syskey )  {
+-pstr P;
++pstr P = NULL;
+   if (syskey==syskey_unix)     
+     P = strrchr(FilePath,'/');
+   else if (syskey==syskey_win) 
+@@ -94,7 +94,7 @@
+ }
+ 
+ cpstr GetFName ( cpstr FilePath, int syskey )  {
+-pstr P;
++pstr P = NULL;
+   if (syskey==syskey_unix)     
+     P = strrchr(FilePath,'/');
+   else if (syskey==syskey_win) 
+@@ -678,7 +678,10 @@
+     }
+     if (TextMode)  {
+       Line[0] = char(0);
+-      fgets ( Line,MaxLen,hFile );
++      if (!fgets ( Line,MaxLen,hFile )) {
++	IOSuccess = False;
++	return 0;
++      }
+       LCnt = strlen(Line);
+       while (LCnt>0)  {
+         if ((Line[LCnt-1]!='\n') &&
+@@ -970,7 +973,6 @@
+ wordUniBin wUB;
+ word       ll;
+ byte       sl;
+-Boolean    B;
+   if (!longLine)  {
+     ReadFile ( &sl,sizeof(sl) );
+     ll = sl;