TLSMD
TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.[1][2] 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.
Contents
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-devellib64xmlrpc0lib64xmlrpc0-devellibcairo2-develglib-gettextizelibglib2.0_0-devellibatk1.0_0-devellibpango1.0_0-devellibgdk_pixbuf2.0_0-devel
LAPACK / BLAS
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.incfile for your system. Below is an example:
SHELL = /bin/sh PLAT = _LINUX FORTRAN = gcc -fPIC -shared OPTS = -funroll-all-loops -O3 DRVOPTS = $(OPTS) NOOPT = LOADER = gcc -fPIC LOADOPTS = TIMER = NONE # not needed ARCH = ar ARCHFLAGS= cr RANLIB = ranlib BLASLIB = ../../blas$(PLAT).a LAPACKLIB= lapack$(PLAT).a TMGLIB = tmglib$(PLAT).a EIGSRCLIB= eigsrc$(PLAT).a LINSRCLIB= linsrc$(PLAT).a
- Enter
SRC/directory and
make
- Enter
BLAS/SRC/directory and
make
Note: The default build will produce lapack_LINUX.a. However, we want a shared object (i.e., lapack.so).
- Create shared object from archive:
nm lapack_LINUX.a|grep gfortran # check that gfortran was used mkdir tmp_lapack; cp lapack_LINUX.a tmp_lapack/; cd tmp_lapack/ ar -x lapack_LINUX.a # extract objects from archive gcc -fPIC -lgfortran -shared *.o -Wl,-soname,lapack.so.3.1.1 -o lapack.so.3.1.1 objdump -p lapack.so.3.1.1 |grep SONAME # should return "lapack.so.3.1.1" ldd lapack.so.3.1.1 # will show you which version of libgfortran was used # Do the same for blas mkdir tmp_blas; cp blas_LINUX.a tmp_blas/; cd tmp_blas/ ar -x blas_LINUX.a gcc -fPIC -lgfortran -shared *.o -W1,-soname,blas.so.3.1.1 -o blas.so.3.1.1 objdump -p blas.so.3.1.1 |grep SONAME ldd blas.so.3.1.1
- 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 lapack.so.3.1.1 /lib64/; cd !$ ln -s /lib64/lapack.so.3.1.1 lapack.so ln -s /lib64/lapack.so.3.1.1 lapack_LINUX.so mv blas.so.3.1.1 /lib64/; cd !$ ln -s /lib64/blas.so.3.1.1 blas.so ln -s /lib64/blas.so.3.1.1 blas_LINUX.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.
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.
References
- ↑ Painter J, Merritt EA (2006). "Optimal description of a protein structure in terms of multiple groups undergoing TLS motion". Acta Cryst, D62(4):439-450. DOI:10.1107/S0907444906005270 .
- ↑ Painter J, Merritt EA (2006). "TLSMD web server for the generation of multi-group TLS models". J Appl Cryst, 39(1):109-111. DOI:10.1107/S0021889805038987
