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.

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.

LAPACK

• Download LAPACK (grab latest version of full package):

wget http://www.netlib.org/lapack/lapack-3.1.1.tgz

• Modify make.inc file for your system.
• Enter SRC/ directory and

make

The default build will produce lapack_LINUX.a. However,

nm blas_LINUX.a|more
nm blas_LINUX.a|grep gfortran_concat_string
nm blas_LINUX.a|grep gfortran
cd BLAS/
cd SRC/
vi Makefile
cd /home/tlsmd/src/other/lapack-3.1.1/
mkdir tmp_blas
cp blas_LINUX.a tmp_blas/
cd tmp_blas/
ar -x blas_LINUX.a
gcc -fPIC -lgfortran -shared *.o -Wl,-soname,blas_LINUX.so -o blas_LINUX.so
objdump -p blas_LINUX.so |grep SONAME
ldd blas_LINUX.so
cp blas_LINUX.so /home/tlsmd/tlsmd/src/
gcc -fPIC -lgfortran -shared *.o -Wl,-soname,lapack_LINUX.so -o lapack_LINUX.so
objdump -p lapack_LINUX.so |grep SONAME
ldd lapack_LINUX.so
cp lapack_LINUX.so /home/tlsmd/tlsmd/src/

Keywords

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

See also

• Python Macromolecular Library (mmLib)

External links

• TLS Motion Determination webserver