Author: bugman
Date: Fri Jan 20 14:53:58 2012
New Revision: 15212
URL: http://svn.gna.org/viewcvs/relax?rev=15212&view=rev
Log:
Merged revisions
14819-14993,14996,14998,15002,15007-15012,15016,15018,15165,15205-15207 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r14819 | bugman | 2011-10-11 10:28:29 +0200 (Tue, 11 Oct 2011) | 6 lines
Added a truncated version of the CaM-KKalpha data from the BMRB 15183 entry
for system tests.
This will be used to validate the Grace plotting when multiple types of
spin are present.
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r14820 | bugman | 2011-10-11 10:53:51 +0200 (Tue, 11 Oct 2011) | 3 lines
Created the test_cam_kkalpha_plot1() system test for checking the grace
plotting of mixed data.
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r14821 | bugman | 2011-10-11 10:58:18 +0200 (Tue, 11 Oct 2011) | 3 lines
Some small fixes for the new test_cam_kkalpha_plot1() system test.
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r14822 | bugman | 2011-10-11 10:59:39 +0200 (Tue, 11 Oct 2011) | 5 lines
Bug fix for the grace.write user function for when the spin ID is specified.
The spin ID was previously unused!
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r14823 | bugman | 2011-10-12 13:07:25 +0200 (Wed, 12 Oct 2011) | 6 lines
The alignment_tensor.fix user function is now tensor specific.
This will allow a subset of tensors to be optimised while the others are
kept fixed. The specific
analysis code will need to be updated for this.
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r14824 | bugman | 2011-10-12 13:12:18 +0200 (Wed, 12 Oct 2011) | 3 lines
Created the generic_fns.align_tensor.all_fixed() fn for determining if all
tensors are fixed.
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r14825 | bugman | 2011-10-12 13:16:14 +0200 (Wed, 12 Oct 2011) | 3 lines
Renamed all_fixed() to all_tensors_fixed().
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r14826 | bugman | 2011-10-12 13:23:23 +0200 (Wed, 12 Oct 2011) | 3 lines
Syntax fix in the all_tensors_fixed() function.
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r14827 | bugman | 2011-10-12 13:24:08 +0200 (Wed, 12 Oct 2011) | 3 lines
Syntax error in the align_tensor.fix user function front end.
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r14828 | bugman | 2011-10-12 13:34:05 +0200 (Wed, 12 Oct 2011) | 3 lines
Updated the relax data store alignment tensor objects to allow for the
per-tensor fixed flag.
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r14829 | bugman | 2011-10-12 13:36:16 +0200 (Wed, 12 Oct 2011) | 5 lines
Updated the N-state model analysis code to handle the per-alignment tensor
fixed flag.
This allows subsets of tensors to be optimised while the others are fixed.
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r14830 | bugman | 2011-10-12 13:54:33 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the N-state model optimisation for when a subset of tensors are
fixed.
The RDC and PCS data was incorrectly assembled.
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r14831 | bugman | 2011-10-12 14:00:19 +0200 (Wed, 12 Oct 2011) | 5 lines
The RDC and PCS Q factor functions are now more robust when data is missing.
The data checks are now more extensive.
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r14832 | bugman | 2011-10-12 14:06:31 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for a divide by zero error in the PCS Q factor function.
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r14833 | bugman | 2011-10-12 14:21:02 +0200 (Wed, 12 Oct 2011) | 3 lines
The RDC and PCS Q factors for each alignment is now stored as a dictionary
in the relax data store.
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r14834 | bugman | 2011-10-12 14:35:47 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the storing of the N-state model back-calculated RDC and PCS data.
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r14835 | bugman | 2011-10-12 14:46:14 +0200 (Wed, 12 Oct 2011) | 5 lines
Fix for the N-state model _minimise_bc_data() method for when no alignments
are present.
This fixes a recently introduced problem.
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r14836 | bugman | 2011-10-12 14:57:13 +0200 (Wed, 12 Oct 2011) | 3 lines
Another fix for a recent bug in _minimise_bc_data().
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r14837 | bugman | 2011-10-12 15:18:25 +0200 (Wed, 12 Oct 2011) | 3 lines
Created a system test script for checking one type of algorithm for Ln3+
position optimisation.
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r14838 | bugman | 2011-10-12 15:32:46 +0200 (Wed, 12 Oct 2011) | 5 lines
Created the test_metal_pos_opt() N-state model system test.
Specific RDC and PCS data for this test has also been generated.
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r14839 | bugman | 2011-10-12 15:40:08 +0200 (Wed, 12 Oct 2011) | 5 lines
Bug fix for the setup of the N-state model target function.
This is triggered by missing data.
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r14840 | bugman | 2011-10-12 16:30:00 +0200 (Wed, 12 Oct 2011) | 5 lines
The N-state model can now be optimised with a subset of the alignment
tensors fixed.
This required a reworking of the data assembly and target function code.
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r14841 | bugman | 2011-10-12 16:30:24 +0200 (Wed, 12 Oct 2011) | 3 lines
Removed an empty line.
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r14842 | bugman | 2011-10-12 16:40:56 +0200 (Wed, 12 Oct 2011) | 3 lines
Updated the metal_pos_opt.py N-state model system test script to catch
another code design problem.
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r14843 | bugman | 2011-10-12 16:47:53 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the population N-state model for when subsets of alignment
tensors are fixed.
This is in the function, gradient, and Hessian code.
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r14844 | bugman | 2011-10-12 16:55:39 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the population N-state model target function.
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r14845 | bugman | 2011-10-12 17:00:24 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the setup of the 2-domain N-state model.
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r14846 | bugman | 2011-10-12 17:19:36 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for all of the N-state models - the indices were not being
incremented!
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r14847 | bugman | 2011-10-12 17:28:48 +0200 (Wed, 12 Oct 2011) | 3 lines
One last fix for the setup of the N-state model target functions.
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r14848 | bugman | 2011-10-12 17:36:19 +0200 (Wed, 12 Oct 2011) | 5 lines
Added another check to the metal optimisation N-state model system test
script.
This now catches if the metal has been optimised when the tensors are fixed.
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r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2 value
of 0 at all times!
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r14850 | bugman | 2011-10-12 17:50:04 +0200 (Wed, 12 Oct 2011) | 5 lines
Added some optimisation speed ups to the metal_pos_opt.py N-state model
system test script.
These are to allow the test to complete in a reasonable time.
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r14851 | bugman | 2011-10-12 17:51:56 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the N-state model minimisation RDC and PCS setup methods.
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r14852 | bugman | 2011-10-12 17:56:04 +0200 (Wed, 12 Oct 2011) | 3 lines
Added some more checks into the metal_pos_opt.py N-state model system test
script.
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r14853 | bugman | 2011-10-12 17:59:41 +0200 (Wed, 12 Oct 2011) | 16 lines
Reverted r14849 as this was not the correct solution to the problem!
The command used was:
svn merge -r14849:r14848 .
.....
r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Changed paths:
M /1.3/maths_fns/n_state_model.py
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2
value of 0 at all times!
.....
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r14854 | bugman | 2011-10-12 18:16:05 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the metal position optimisation test data.
The RDCs and PCSs were 3 times too large!
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r14855 | bugman | 2011-10-12 18:17:56 +0200 (Wed, 12 Oct 2011) | 3 lines
A fix for the previous fixes for the metal position optimisation test data!
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r14856 | bugman | 2011-10-12 18:19:28 +0200 (Wed, 12 Oct 2011) | 3 lines
The chi2 of zero test in the metal_pos_opt.py system test script is now not
exact.
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r14857 | bugman | 2011-10-12 18:22:29 +0200 (Wed, 12 Oct 2011) | 3 lines
Added another chi2 of zero check to the metal_pos_opt.py system test script.
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r14858 | bugman | 2011-10-12 18:31:16 +0200 (Wed, 12 Oct 2011) | 3 lines
Added a check that the chi2 value is no longer zero if the Ln3+ is moved in
the metal_pos_opt.py test.
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r14859 | bugman | 2011-10-12 18:54:15 +0200 (Wed, 12 Oct 2011) | 3 lines
More attempts at fixing the N-state model code.......
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r14860 | bugman | 2011-10-12 18:54:49 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the position checking in the metal_pos_opt.py script.
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r14861 | bugman | 2011-10-12 18:57:31 +0200 (Wed, 12 Oct 2011) | 6 lines
Reverted the last revision (r14860) as the change was rubbish.
The command used was:
svn merge -r14860:r14859 .
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r14862 | bugman | 2011-10-12 19:01:27 +0200 (Wed, 12 Oct 2011) | 3 lines
More fixes and improvements to the test_metal_pos_opt() system test.
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r14863 | bugman | 2011-10-12 19:07:04 +0200 (Wed, 12 Oct 2011) | 23 lines
Revert the reversion of revision r14853 which was a reversion of r14849, as
it was ok!
The command used was:
svn merge -r14853:r14852 .
.....
Reverted r14849 as this was not the correct solution to the problem!
The command used was:
svn merge -r14849:r14848 .
.....
r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Changed paths:
M /1.3/maths_fns/n_state_model.py
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2
value of 0 at all times!
.....
.....
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r14864 | bugman | 2011-10-12 19:12:19 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the N-state model optimisation set up if PCS or RDC data is not
loaded.
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r14865 | bugman | 2011-10-12 19:16:18 +0200 (Wed, 12 Oct 2011) | 3 lines
Clean up of the metal_pos_opt.py system test script.
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r14866 | bugman | 2011-10-12 19:31:40 +0200 (Wed, 12 Oct 2011) | 3 lines
Removed the Q factor calculations from metal_pos_opt.py as they should
already be calculated.
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r14867 | bugman | 2011-10-12 19:32:04 +0200 (Wed, 12 Oct 2011) | 3 lines
Some last fixes, hopefully, for the N-state model code.
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r14868 | bugman | 2011-10-13 18:31:08 +0200 (Thu, 13 Oct 2011) | 3 lines
Fix for the paramag.centre user function when a numpy array is used.
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r14869 | bugman | 2011-10-14 10:21:50 +0200 (Fri, 14 Oct 2011) | 6 lines
Fix for a problem introduced at r14810 - relax uses D and not 2D internally
for the RDCs.
This is only a problem if the rdc.read 'data_type' argument is used. This
is only a few days old so
will affect no one!
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r14870 | bugman | 2011-10-14 16:31:45 +0200 (Fri, 14 Oct 2011) | 6 lines
Bug fix allowing relax to be run in profiling mode.
This still does not work as the multi-processor branch has broken this
coding and debugging
functionality.
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r14871 | bugman | 2011-10-14 16:37:52 +0200 (Fri, 14 Oct 2011) | 6 lines
Bug fix for the profiling!
This coding and debugging functionality now works again. This has been
broken since the merger of
the multi-processor branch.
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r14872 | bugman | 2011-10-14 20:29:51 +0200 (Fri, 14 Oct 2011) | 5 lines
Increased the efficiency of the relax data store spin system creation.
This becomes noticeable when large numbers of structures are read into
relax.
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r14873 | bugman | 2011-10-17 13:59:57 +0200 (Mon, 17 Oct 2011) | 6 lines
Added the bc flag to the RDC and PCS display and write user function
front-ends.
This This will allow the back-calculated data to be displayed or written
rather than the measured
values.
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r14874 | bugman | 2011-10-17 14:09:51 +0200 (Mon, 17 Oct 2011) | 5 lines
Updated the RDC and PCS display and write user function backends for the
new bc flag.
This allows access to the back-calculated rather than measured data.
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r14875 | bugman | 2011-10-17 18:31:38 +0200 (Mon, 17 Oct 2011) | 3 lines
Created a system test with RDC data for loading RDCs from a file with spin
ID strings at the start.
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r14876 | bugman | 2011-10-18 08:51:59 +0200 (Tue, 18 Oct 2011) | 5 lines
Bug fix for the relax_io.read_spin_data() function for spin IDs.
Spin IDs can now be handled if they are the first column in the data file!
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r14877 | bugman | 2011-10-18 09:13:22 +0200 (Tue, 18 Oct 2011) | 7 lines
The rdc and pcs display and write user functions now output mol, res, and
spin name and num cols.
Instead of the spin ID column, these user functions now output the molecule
name, residue name,
residue number, spin name and spin number columns. This is better to read
back into relax as info
such as the spin number can be ignored to allow different PDB files to be
used.
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r14878 | bugman | 2011-10-18 10:39:11 +0200 (Tue, 18 Oct 2011) | 5 lines
Created the alignment tensor module num_tensors() method for counting
tensors.
This excludes fixed tensors by default.
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r14879 | bugman | 2011-10-18 10:47:58 +0200 (Tue, 18 Oct 2011) | 5 lines
Created the alignment tensor module return_tensor() function for returning
tensors.
This takes fixed tensors into account, skipping them if the skip_fixed flag
is set.
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r14880 | bugman | 2011-10-18 11:09:31 +0200 (Tue, 18 Oct 2011) | 3 lines
The N-state model Monte Carlo simulations can now handle fixed alignment
tensors.
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r14881 | bugman | 2011-10-18 15:46:27 +0200 (Tue, 18 Oct 2011) | 6 lines
Fix for the set up of Monte Carlo data for fixed alignment tensors in the
N-state model.
The _minimise_setup_fixed_tensors() method has been fixed to return the
actual tensor rather than
simulation for the fixed tensors, as there is no simulation tensor in that
case.
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r14882 | bugman | 2011-10-21 11:12:39 +0200 (Fri, 21 Oct 2011) | 5 lines
Fix for the frame_order.cone_pdb user function.
The create_cone_pdb was referencing a non-existent variable!
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r14883 | bugman | 2011-10-23 18:51:42 +0200 (Sun, 23 Oct 2011) | 11 lines
Added a few new RelaxError classes.
These include:
RelaxNoneListFloatError
RelaxMatrixFloatError
RelaxNoneMatrixFloatError
The BaseArgError class was also modified to handle the length arg (now the
size arg) being a tuple
for matrix sizes.
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r14884 | bugman | 2011-10-23 18:55:01 +0200 (Sun, 23 Oct 2011) | 7 lines
Added a few new argument checks for arrays and matrices of floats.
These are:
is_float_array()
is_float_matrix()
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r14885 | bugman | 2011-10-23 18:56:36 +0200 (Sun, 23 Oct 2011) | 6 lines
Created the front end for the new structure.rotate user function.
The purpose of this user function is to apply arbitrary rotations to the
structures loaded into
relax about a given origin.
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r14886 | bugman | 2011-10-23 18:58:00 +0200 (Sun, 23 Oct 2011) | 3 lines
Created the back end for the structure.rotate user function.
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r14887 | bugman | 2011-10-23 19:03:51 +0200 (Sun, 23 Oct 2011) | 5 lines
Started to create some data for testing the frame order theory.
This will be used to generate synthetic data for all 9 models currently in
relax.
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r14888 | bugman | 2011-10-23 19:05:50 +0200 (Sun, 23 Oct 2011) | 3 lines
Created the RDC and PCS test data for the rigid frame order model.
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r14889 | bugman | 2011-10-23 22:08:25 +0200 (Sun, 23 Oct 2011) | 3 lines
Errors are now set on the RDCs and PCSs.
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r14890 | bugman | 2011-10-24 00:29:08 +0200 (Mon, 24 Oct 2011) | 3 lines
Updated the alignment tensor fitting script.
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r14891 | bugman | 2011-10-24 09:35:29 +0200 (Mon, 24 Oct 2011) | 3 lines
Small fix for the tensor fitting script, and addition of the log file and
output tensors.
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r14892 | bugman | 2011-10-24 11:59:51 +0200 (Mon, 24 Oct 2011) | 5 lines
Added a script for optimising the rigid frame order CaM test data.
The resultant average position PDB file and relax save file have also been
added for reference.
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r14893 | bugman | 2011-10-24 12:11:07 +0200 (Mon, 24 Oct 2011) | 3 lines
Created the Frame_order.test_cam_rigid system test and optimisation script.
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r14894 | bugman | 2011-10-24 12:24:51 +0200 (Mon, 24 Oct 2011) | 6 lines
Modified the rigid frame order CaM test model script to properly test the
PyMOL representation.
This is not a system test, but is to be used manually and visually to check
that the PyMOL
representation created by relax of the average position, eigenframe, and
cone is correct!
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r14895 | bugman | 2011-10-24 12:25:32 +0200 (Mon, 24 Oct 2011) | 3 lines
Created a data directory for the free rotor CaM test model.
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r14896 | bugman | 2011-10-24 14:58:21 +0200 (Mon, 24 Oct 2011) | 5 lines
Created a PDB distribution of CaM orientations for the free rotor frame
order model.
This is a uniform set of rotations about the pivot-CoM axis.
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r14897 | bugman | 2011-10-24 15:01:05 +0200 (Mon, 24 Oct 2011) | 5 lines
The structure.rotate user function can now operate in individual structural
models.
The model keyword argument has been added to allow this.
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r14898 | bugman | 2011-10-24 15:01:47 +0200 (Mon, 24 Oct 2011) | 3 lines
The structure.write_pdb user function can now create compressed (bzip2 or
gzip) PDB files.
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r14899 | bugman | 2011-10-24 15:10:52 +0200 (Mon, 24 Oct 2011) | 3 lines
Back calculated the RDC and PCS test data from the CaM free rotor frame
order model.
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r14900 | bugman | 2011-10-24 15:31:02 +0200 (Mon, 24 Oct 2011) | 3 lines
Calculated the pure RDC tensors for the free rotor CaM frame order model.
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r14901 | bugman | 2011-10-24 15:34:04 +0200 (Mon, 24 Oct 2011) | 3 lines
The structure.read_pdb user function can now handle bzip2 or gzip
compressed PDB files.
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r14902 | bugman | 2011-10-24 15:44:36 +0200 (Mon, 24 Oct 2011) | 3 lines
Added the frame order free rotor optimisation script and its results.
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r14903 | bugman | 2011-10-24 16:09:00 +0200 (Mon, 24 Oct 2011) | 3 lines
Created a script for animating the CaM free rotor frame order model test
data in PyMOL.
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r14904 | bugman | 2011-10-24 16:35:42 +0200 (Mon, 24 Oct 2011) | 3 lines
Created the Frame_order.test_cam_free_rotor system test for the CaM
synthetic data.
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r14905 | bugman | 2011-10-24 17:52:04 +0200 (Mon, 24 Oct 2011) | 3 lines
Added checks for the n_state_model.cone_pdb user fn in the
N_state_model.test_5_state_xz system test.
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r14906 | bugman | 2011-10-24 17:52:47 +0200 (Mon, 24 Oct 2011) | 5 lines
Bug fixes for the n_state_model.cone_pdb user function.
The code was old and not functional any more.
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r14907 | bugman | 2011-10-24 17:55:26 +0200 (Mon, 24 Oct 2011) | 5 lines
Bug fix for the pymol.cone_pdb user function for when there is no average
domain position.
This is necessary for the old 2-domain N-state model analysis type.
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r15212 - in /branches/cst: ./ auto_analyses/ data/ docs/ generic_fns/ generic_fns/structure/ gui/user_functions/ maths_fns/ ...