Tutorial for model free SBiNLab - Revision history

Tlinnet: /* Pymol macro */

2017-10-22T10:40:52Z

Pymol macro

Tlinnet: /* Background */

2017-10-22T10:40:30Z

Background

Tlinnet: /* Background */

2017-10-22T10:39:08Z

Background

Tlinnet: /* Background */

2017-10-22T10:38:00Z

Background

Tlinnet: /* 13_Model_2-5 - Run Model 2 to 5 */

2017-10-22T10:30:11Z

13_Model_2-5 - Run Model 2 to 5

Tlinnet: /* 12_Model_1_I_local_tm.py - Only run local_tm */

2017-10-22T10:29:40Z

12_Model_1_I_local_tm.py - Only run local_tm

Tlinnet: /* Prepare data */

2017-10-22T07:47:34Z

Prepare data

Tlinnet: /* Prepare data */

2017-10-22T07:40:37Z

Prepare data

Tlinnet: /* Prepare data */

2017-10-22T07:21:04Z

Prepare data

Tlinnet: /* Pymol macro */

2017-10-21T09:11:15Z

Pymol macro

@@ Line 405: / Line 405: @@
 See here for info how the macro is applied
-* [http://www.nmr-relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of value to pymol macro]
+* [http://www.nmr-relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
 Run with

@@ Line 9: / Line 9: @@
 * [http://www.nmr-relax.com/manual/Model_free_analysis.html Link to the manual]
 * [http://www.nmr-relax.com/manual/The_model_free_models.html Summary of model-free models]
 * d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
 * d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]

@@ Line 7: / Line 7: @@
 For references, see [http://www.nmr-relax.com/refs.shtml relax references]:
 * [[Model-free_analysis_single_field#Protocol|See this description of the protocol by Edward]] and image [http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html The diffusion seeded paradigm]
 * [http://www.nmr-relax.com/manual/The_model_free_models.html Summary of model-free models]
 * d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
 * d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]

@@ Line 7: / Line 7: @@
 For references, see [http://www.nmr-relax.com/refs.shtml relax references]:
 * [[Model-free_analysis_single_field#Protocol|See this description of the protocol by Edward]] and image [http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html The diffusion seeded paradigm]
 * [http://www.nmr-relax.com/manual/Model_free_analysis.html Link to the manual]
 * d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]

@@ Line 331: / Line 331: @@
 relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
 # Or
-mpirun -np 4 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
+mpirun -np 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
 # When relax is running, push: Ctrl+b and then d, to disconnect without exit
@@ Line 341: / Line 341: @@
 relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
 # Or
-mpirun -np 4 relax --multi='mpi4py' 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
+mpirun -np 5 relax --multi='mpi4py' 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
 </source>
@@ Line 349: / Line 349: @@
 relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
 # Or
-mpirun -np 4 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
+mpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
 </source>
@@ Line 357: / Line 357: @@
 relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
 # Or
-mpirun -np 4 relax --multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
+mpirun -np 5 relax --multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
 </source>

@@ Line 305: / Line 305: @@
 # or
-tmux new -s m1_multi
+tmux new -s m1
-mpirun -np 12 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
+mpirun -np 22 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
 </source>

@@ Line 215: / Line 215: @@
 # Make deselection
 echo "#" > deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t158" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t157" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t17" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t159" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t59" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t98" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t76" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t155" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t156" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t120" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t49" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t48" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
-cat R1_600MHz_new_model_free.dat | grep -e "ArcCALD\t154" >> deselect.txt
+cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
 </source>
 |}