TLSMD

TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning the protein chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a specified maximum number of TLS groups. Each trial partition is evaluated by how well it predicts the observed atomic displacement parameters (ADPs, "thermal parameters") that came out of crystallographic refinement.

Note: On 2008-02-15, we released version 1.0.0 of tlsmd. It is available for download on sourceforge.

Installation

Note: This section will cover the install of pymmlib, including tlsmd, on a 64-bit system running Mandriva Linux 2007.1. However, most of it should work for 32-bit systems and any other Linux distribution.

It is best to get the package as follows:

svn co https://pymmlib.svn.sourceforge.net/svnroot/pymmlib/trunk pymmlib

Dependencies

Note: It very much depends if you are running on a 32- or 64-bit machine. So, instead of, say "liblapack" (32-bit), you would install "lib64lapack" (64-bit)

• Python (>= 2.4): python + libpython2.5-devel (if using Python 2.5)
• NumPy (>= 0.9.6): python-numpy + python-numpy-devel
• PyOpenGL: python-opengl
• Gtk+-2.2 or Gtk+-2.4: libgtk+2.0_0-devel
• PyGTK (>= 2.x): pygtk2.0-devel + python-gtkglext
• GtkGlExt: lib64gtkglext-devel
• PyGtkGLExt: libgtkglext-1.0_0 + libgtkglext-1.0_0-devel
• Python Imaging Library (>= 1.1.5): python-imaging-devel
• CherryPy: python-cherrypy
• LAPACK (see section below; >= 3.0): lapack + liblapack3.0-devel
• ATLAS (>= 3.6.0): atlas
• MINPACK
• Other
  • lib64xmu6-devel
  • lib64xmlrpc0
  • lib64xmlrpc0-devel
  • libcairo2-devel
  • glib-gettextize
  • libglib2.0_0-devel
  • libatk1.0_0-devel
  • libpango1.0_0-devel
  • libgdk_pixbuf2.0_0-devel

LAPACK

Note: See Installation Guide for LAPACK for detailed information.

• Download LAPACK (grab latest version of full package; must be at least >=3.0.0):

wget http://www.netlib.org/lapack/lapack.tgz
tar xvf lapack.tgz && cd lapack-3.1.1/

• Modify make.inc file for your system. Below is an example:

SHELL    = /bin/sh
PLAT     = _LINUX
FORTRAN  = gcc -fPIC -shared
OPTS     = -funroll-all-loops -O3
DRVOPTS  = $(OPTS)
NOOPT    =
LOADER   = gcc -fPIC
LOADOPTS =
TIMER    = EXT_ETIME
ARCH     = ar
ARCHFLAGS= cr
RANLIB   = ranlib
BLASLIB  = ../../blas$(PLAT).a
LAPACKLIB= lapack$(PLAT).a
TMGLIB   = tmglib$(PLAT).a
EIGSRCLIB= eigsrc$(PLAT).a
LINSRCLIB= linsrc$(PLAT).a

• Enter SRC/ directory and

make

Note: The default build will produce lapack_LINUX.a. However, we want a shared object (i.e., lapack_LINUX.so).

• Create shared object from archive:

nm blas_LINUX.a|grep gfortran  # check that gfortran was used
mkdir tmp_blas; cp blas_LINUX.a tmp_blas/; cd tmp_blas/
ar -x blas_LINUX.a  # extract objects from archive
gcc -fPIC -lgfortran -shared *.o -W1,-soname="blas.so" -o blas.so.3.1.1
objdump -p blas_LINUX.so |grep SONAME  # should return "blas.so"
ldd blas_LINUX.so   # will show you which version of libgfortran was used

# Do the same for lapack
mkdir tmp_lapack; cp lapack_LINUX.a tmp_lapack/; cd tmp_lapack/
ar -x lapack_LINUX.a
gcc -fPIC -lgfortran -shared *.o -Wl,-soname,lapack.so -o lapack_LINUX.so
objdump -p lapack_LINUX.so |grep SONAME
ldd lapack_LINUX.so

• Update your /etc/ld.so.cache (make sure the absolute path of your newly created shared libraries are in /etc/ld.so.conf):

ldconfig  # as root

• Symlinks: Instead of doing the following:

mv blas_LINUX.so /lib64/blas.so.3.1.1; cd !$
ln -s /lib64/blas.so.3.1.1 blas.so
mv lapack_LINUX.so /lib64/lapack.so.3.1.1; cd !$
ln -s /lib64/lapack.so.3.1.1 lapack.so

you can let ldconfig take care of it, iff you have correctly labeled SONAME's in the shared libraries you just built.

Build

python setup.py buildlib
python setup.py checkdeps  # if all is good, then
python setup.py build      # if all is good, then
python setup.py install    # as root

Set the PYTHONPATH environment variable:

export PYTHONPATH=/usr/bin/python:$HOME/tlsmd/pymmlib:$HOME/tlsmd/pymmlib/mmLib

tlsmdmodule.so

Make the necessary changes to:

tlsmd/src/Makefile

Then,

make
make install  # creates tlsmdmodule.so and copies it to tlsmd/bin/

conf.py

Make the necessary changes to the following file:

tlsmd/bin/tlsmdlib/conf.py

Resources

SONAME 

a soname is a field of data in a shared object file. The soname provides version backwards-compatibility information to the system. For instance, if a program requests to use version 1.0 of a shared object but the system only includes version 2.0 of that shared object, the soname field of the shared object tells the system whether it is usable in the place of version 1.0.

• Shared Libraries
• Library-related Commands and Files

ranlib

ranlib generates an index to the contents of an archive and stores it in the archive. The index lists each symbol defined by a member of an archive that is a relocatable object file.

You may use nm -s or nm --print-armap to list this index.

An archive with such an index speeds up linking to the library and allows routines in the library to call each other without regard to their placement in the archive.

The GNU ranlib program is another form of GNU ar; running ranlib is completely equivalent to executing ar -s.

Keywords

TLSMD; TLS motion; web server; computer programs; TLS, translation libration screw; macromolecular crystallography; protein crystallography.

See also

• Python Macromolecular Library (mmLib)
• DynDom — a program to determine domains, hinge axes, and hinge bending residues in proteins where two conformations are available.
• ar — create, modify, and extract from archives.
• nm — list symbols from object files.
• ranlib — generate index to archive.

External links

• TLS Motion Determination webserver