Difference between revisions of "TLSMD"
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'''TLS Motion Determination''' ('''TLSMD''') analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.<ref name="Painter2006a">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/Acta_D62_439.pdf Optimal description of a protein structure in terms of multiple groups undergoing TLS motion]". ''Acta Cryst, D62(4):439-450''. {{doi|10.1107/S0907444906005270}}.</ref><ref name="Painter2006b">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/JApplCryst_39_109.pdf TLSMD web server for the generation of multi-group TLS models]". ''J Appl Cryst, 39(1):109-111''. {{doi|10.1107/S0021889805038987}}</ref> 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. | '''TLS Motion Determination''' ('''TLSMD''') analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.<ref name="Painter2006a">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/Acta_D62_439.pdf Optimal description of a protein structure in terms of multiple groups undergoing TLS motion]". ''Acta Cryst, D62(4):439-450''. {{doi|10.1107/S0907444906005270}}.</ref><ref name="Painter2006b">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/JApplCryst_39_109.pdf TLSMD web server for the generation of multi-group TLS models]". ''J Appl Cryst, 39(1):109-111''. {{doi|10.1107/S0021889805038987}}</ref> 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 <nowiki>http://www.netlib.org/lapack/lapack-3.1.1.tgz</nowiki> | ||
| + | |||
| + | *Modify <code>make.inc</code> file for your system. | ||
| + | *Enter <code>SRC/</code> directory and | ||
| + | make | ||
| + | The default build will produce <code>lapack_LINUX.a</code>. 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== | ==Keywords== | ||
Revision as of 00:54, 28 August 2007
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.
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.incfile 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)
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
