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ChangeLog
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2024-04-22 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.08
2024-01-17 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.07
2024-01-15 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.06
2024-01-15 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.05
2024-01-14 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.04
2023-12-22 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.03
2023-11-10 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.02
2023-11-09 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1.01
2023-10-31 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.1
2022-04-14 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.0.04
2022-04-12 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.0.03
2022-04-04 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1.0.01
2022-04-01 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 1
2024-04-22 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.94
2024-01-09 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.93
2023-09-04 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.92
2023-08-04 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.91
2023-07-25 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.9
2023-06-23 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.8
2023-01-02 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.7
2022-12-05 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.6
2022-10-01 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.5
2022-09-17 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.4
2022-05-31 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.2
2022-03-18 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8.1
2022-03-01 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.8
2022-01-24 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.7
2021-07-02 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.6
2021-03-16 Paul Emsley <pemsley at mrc dash lmb dot cam ac dot uk>
* Release 0.9.5
2021-02-02 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9.4.1
2021-01-29 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9.4
2020-10-18 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9.3
2020-10-02 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9.2
2020-09-25 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9.1
2020-04-01 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.9
2018-04-01 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.9.2
2018-03-18 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.9.1
2018-01-09 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.9
2017-03-13 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.8
2016-11-07 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.7
2016-08-18 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.6
2016-08-08 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.5
2016-07-28 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.4
2016-04-01 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.3
2015-08-27 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.2
2013-12-10 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8.1
2013-05-14 Paul Emsley <pemsley at mrc dash lmb dot ac dot uk>
* Release 0.8
2013-05-14 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.7.1
2012-09-28 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.7
2010-01-26 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.6.1
2009-12-01 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.6
2008-12-15 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.5.2, fix silly shift labelling atoms bug.
* Release 0.5.1
2008-09-24 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.5
2008-01-02 Paul Emsley <paul.emsley@bioc.ox.ac.uk>
* Release 0.4
2007-07-12 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info.h: add geom_p->add_planar_peptide_restraint()
to graphics_info_t::init().
2007-07-11 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/globjects.cc: changed smooth_scroll_step to 80 from 8.
2007-06-29 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.3.2
2007-06-26 Paul Emsley <emsley@ysbl.york.ac.uk>
* coot-utils/coot-shelx-ins.cc: (make_atom): set the U matrix
correctly. There was a transposition of u12 and u23. Ouch.
2007-06-16 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc: (add try/catch mechanism round
file.open_read() in read_ccp4_map()). Fixes a crash on reading a
non-CCP4 map.
2007-06-21 Paul Emsley <emsley@localhost>
* db-main/db-main.cc (clear_results): clear the output fragment
too.
2007-06-18 Paul Emsley <emsley@localhost>
* src/c-interface.cc: Add action view - as a direct view. But,
don't we really instead want to insert such a thing into a set of
views that we already have?
2007-06-17 Paul Emsley <emsley@localhost>
* ligand/wiggly-ligand.cc: turn off debugging for wiggly ligands.
2007-06-07 Paul Emsley <emsley@ysbl.york.ac.uk>
* coords/Bond_lines.cc: (construct_from_atom_selection): Don't
mark S, SE, CL, BR, or P as bonded.
2007-05-29 Paul Emsley <emsley@localhost>
* src/molecule-class-info-other.cc:
change_chain_id_with_residue_range_helper_insert_or_add() the
target_residue should simply be a residue that will appear in the
pdb file before the inserted residue.
2007-05-18 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (hardware_stereo_mode): kill off the
SIDE_BY_SIDE_STEREO widget, if it was active.
2007-05-12 Paul Emsley <emsley@localhost>
* src/c-interface-build.cc (get_monomer): check that the library
does not provide the restraints for the given 3-letter-code before
passing to the libcheck function [Judit Debreczeni].
2007-05-04 Paul Emsley <emsley@localhost>
* src/molecule-class-info.cc: (anisotropic_atoms): Add in cholesky
decomposition to the matrix.
2007-05-03 Paul Emsley <emsley@localhost>
* src/graphics-info-modelling.cc: Added
execute_simple_nucleotide_addition() function.
2007-05-01 Paul Emsley <emsley@localhost>
* src/molecule-class-info.cc: Kevin Cowtan provided a patch for
CNS map reading.
2007-04-13 Paul Emsley <emsley@localhost>
* src/pick.cc: Added Segid info to picked atom output info
[Christie Durnham]
2007-04-07 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.3.1
* enable NCS ghosts. Add fractional matrix for LSQing.
* Release 0.3
2007-03-31 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info.cc: (destroy_edit_backbone_rama_plot): set
edit_phi_psi_plot to null so that it is not left dangling when we
do edit phi/psi the the N-terminal residue, where there is no
Ramachandran plot made. Fixes Richard Baxter bug.
(update_molecule_to): don't call molecule_class_info_t's
update_molecule_to if there are no atoms in the guide point
vector. This stops the creation of a molecule with no atoms in
it, which causes problems because it seems to be closed. Also
this means that the model is not modified without creating a new
atom selection. Fixes Richard Baxter bug.
2007-03-19 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/cc-interface.hh: Add USE_GUILE protection to
dictionaries_read().
2007-03-06 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface-build.cc: (replace_fragment): function added.
2007-03-05 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface.h: (zoom_factor) function added.
2007-02-13 Paul Emsley <emsley@ysbl.york.ac.uk>
* mapview.glade: Fix typo in "No Restraints" window [Steven
Sheriff].
2007-02-10 Paul Emsley <emsley@ysbl.york.ac.uk>
* configure.in: Changed to version 0.2.1-pre-2 as I manually apply
diffs from Paris.
2007-02-08 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/callbacks.c: Many functions: change return types from gchar*
to const char * [typically from entries] to compile cleanly with
GTK2.
* src/c-interface-info.cc:
(generic_string_vector_to_list_internal): needs USE_GUILE
protection.
* macros/guile-gtk.m4 (AM_PATH_GUILE_GTK): Use coot_gtk2 to set
the version of libguilegtk-x.y.la for GUILE_GTK_LIBS.
2007-02-07 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/Makefile.am (INCLUDES): reordered because we want GTK flags
and GUILE flags to come first because they could be in a different
directory - when test building.
* src/molecule-class-info-other.cc: (get_term_type) return
"singleton" as a possible terminal residue type.
* ligand/residue_by_phi_psi.cc: (residue_by_phi_psi) and other
functions: add support for terminus type "singleton". Treat as a
C-terminal addition.
* src/graphics-info-modelling.cc:
(execute_rotate_translate_ready): change the code path to check
for atoms being in the same chain before putting up the GUI and
making an intermediate molecule.
* src/graphics-info-modelling.cc:
(execute_rigid_body_refine): change the code path to check for
atoms being in the same chain before doing rigid body refine. Does
that fix Bob Nolte's bug?
2007-01-30 Paul Emsley <emsley@ysbl.york.ac.uk>
* ligand/rigid-body.cc: (rigid_body_fit): Assign a (0,0,0)
grad_vec when the occupancy of the atom is 0, otherwise it was
undefined. Fixes crazy alpha helix placement?
2007-01-04 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.2
2006-12-05 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info-state.cc: (save_state_file) save the map
sampling rate if it not the default.
2006-11-06 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (dragged_refinement_steps_per_frame): return
the number of steps so that we can save them.
2006-11-02 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface-build.cc: (set_show_chi_angle_bond): Add a
redraw so that the new mode of chi angle drawing [typically called
from callbacks.c functions] are made effective [green bond no
longer left behind].
* src/c-interface-preferences.cc:
(save_accept_reject_dialog_window_position): only [dereference and]
save the position if the dialog is not null.
2006-11-03 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc: (handle_read_draw_molecule): only
update the bond width if this is NOT a undo.
2006-09-17 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info-modelling.cc: (rot_trans_adjustment_changed):
add in code to check for CA bonds in master molecule and find
bonds appropriately.
* src/molecule-class-info.cc: remove intermediate pair of Cartesians
in draw_skeleton(), suggestion from Ezra Peisach.
2006-08-31 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/globjects.cc (key_press_event): mark as handled GDK_Meta_L
and GDK_Meta_R [for mac].
2006-08-23 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* Release 0.1.2.
2006-08-24 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/callbacks.c (on_auto_open_mtz_activate): correctly set the
sort_button [fixes random crash maybe].
* ligand/ligand.cc: ligand constructor: Change the default
map_atom_mask_radius to 2.0A.
2006-08-20 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface.cc: also c-interface-preferences.cc and
globjects.cc, callback.c and graphics-info-state.cc: Add code to
store, save and restore the position of the ramachandran plot.
2006-08-19 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info-ncs.cc: (copy_residue_range): completely
re-written to fix bug noted by Panagis Filippakopoulos.
2006-08-14 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface-preferences.cc: (Add functions to save the
position of major widgets).
2006-08-08 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/globjects.cc: (handle_scroll_event): abstracted from long
glarea_button_press [More of the same please!]. Now scroll_events
[GTK2?] are handled similarly.
2006-08-08 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/geometry-graphs.cc:
(render_geometry_distortion_blocks_internal): Use sane_occupancy
to convert from shelx occupancies. Stops geometry distortions
going negative.
* src/c-interface.cc: function to set the default bond thickness,
saved/used in save_state_file().
* src/c-interface-build.cc: (on_merge_molecules_check_button_toggled):
Use GPOINTER_TO_INT to type user data. LTE bug.
* src/c-interface-build.cc (execute_refmac): Use GPOINTER_TO_INT
to get user data from active item. LTE bug.
* src/c-interface.cc (on_filename_filter_toggle_button_toggled):
Use GPOINTER_TO_INT to type user data. LTE bug.
* src/graphics-info-modelling.cc: (rot_trans_adjustment_changed):
Use GPOINTER_TO_INT to type user_data. LTE bug.
2006-08-07 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info.cc: (on_change_current_chi_button_clicked):
use GPOINTER_TO_INT to type user data. LTE bug.
(difference_map_peaks_neighbour_peak): user GPOINTER_TO_INT to
type result of gtk_object_get_user_data(). LTE bug.
(rotamer_dialog_neighbour_rotamer): user GPOINTER_TO_INT to type
user_data. LTE bug.
(bonds_colour_rotation_adjustment_changed): use
GPOINTER_TO_INT. LTE bug.
2006-08-04 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info.cc: (float_to_string): Valgrind was
complaining about uninitialized memory. Not sure why. Index the
arrays to 99 instead when zeroing.
* coords/Bond_lines.cc: (construct_from_asc): when outputing UDD
error for atom [it sholdn't happen] index the correct array. Valgrind
2006-08-03 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc: (label_atom): only draw the atom
labels if the molecule is being displayed.
* src/geometry-graphs.cc:
(render_geometry_distortion_blocks_internal): Don't do things for
atom index -1 [Not sure why atom index *is* -1 though]. This and
below fixes bug on geometry validation of 1HJ9 [Ulrich Englich].
* ideal/simple-restraint.cc: (distortion_score_plane_internal):
Don't do things for atom index -1.
2006-07-24 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* doc/user-manual.texi (masks): mask-map-by-molecule not
mask-map-by-protein.
* src/graphics-info-defines.cc: (check_if_in_pepflip_define): do a
redraw of the graphics after a pepflip.
2006-07-22 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* macros/glut.m4 (AM_PATH_GLUT): Add i686-apple-darwin* option.
2006-07-17 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* coot-utils/coot-shelx-ins.cc: move the precision setting out of
the format statement [ooops!] - fixes Doug Kuntz bug.
2006-07-28 Paul Emsley <emsley@ysbl.york.ac.uk>
* build-it: Fix position of test of status of making guile.
* README: Removed the joke at the start of the README. It is
stale and misleading and I am not sure anyone got the joke (the
URL no longer gave a useful page).
2006-06-23 Paul Emsley <emsley@ysbl.york.ac.uk>
* ligand/find-ligand.cc (main): add wiggly [flexible] ligand option.
* src/molecule-class-info-other.cc: (delete_residue_with_altconf):
when we have a shelxl molecule with just 1 alt conf left, set the
remaining occs to 11.0.
2006-06-16 Paul Emsley <emsley@ysbl.york.ac.uk>
* coords/Bond_lines.cc: (construct_from_asc): Don't draw unbonded
hydrogens if the we are not drawing hydrogens. Fixed bug of
Donnie B.
2006-06-22 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* ligand/ideal-rna.cc: (make_molecule): put the antisense residues
in the chain in reverse order [so that they appear in the pdb file
in increasing order] by using a vector of residues.
2006-06-08 Paul Emsley <emsley@localhost>
* sequence-view/sequence-view.cc: (mol_to_canvas): check that
strand is non-null before doing anything with it. Fixes crash
with 1h5w reported by Roeland Boer [rbocri@cid.csic.es].
2007-06-05 Paul Emsley <emsley@ysbl.york.ac.uk>
* ideal/simple-restraint.cc: (find_link_type): Allow D-peptides as
well as L-peptides.
2006-06-05 Paul Emsley <emsley@ysbl.york.ac.uk>
* geometry/protein-geometry.cc: (init_standard): use CLIBD_MON if
it is set.
2006-06-04 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info-widget-work.cc:
(fill_ncs_control_frame_internal): don't test for display_it_flag
before setting the toggle button. [Actually, that whole frame
should be desensitised according to display_it button state].
2006-05-24 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface.h: enable documentation for superpose functions.
2006-05-22 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface.cc:
read_phs_and_make_map_using_cell_symm_from_mol renamed to
read_phs_and_make_map_using_cell_symm_from_mol_using_implicit_phs_filename.
read_phs_and_make_map_using_cell_symm_from_previous_mol created.
read_phs_and_make_map_using_cell_symm_from_mol created. So that
putting phs data on the command line will use the given pdb.
command line data handling needs to be call this function.
(add_filename_filter_button): filter button created.
(set_file_selection_pre_filtered): function created. To satisfy
Phil, I think.
* coot-utils/coot-shelx-ins.cc: (write_ins_file): use precision(9)
when outputting coords - stops [unreadable] accidental exponential
output formatting.
* src/c-interface-build.cc: (set_undo_molecule): Allow the setting
of the undo molecule to a molecule that might have 0 selected
atoms [e.g. we have a ligand as a molecule and accidently delete
it]
2006-05-21 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface-build.cc: (ideal_nucleic_acid): downcase the
sequence.
2006-05-30 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (get_text_for_aniso_limit_radius_entry):
don't write over the end of the malloced memory.
2006-05-19 Paul Emsley <emsley@ysbl.york.ac.uk>
* Release 0.1.1
2006-05-15 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface-build.cc:
(save_symmetry_coords_from_fileselection): remove origin pre-shift
from trans of symm atom before writing coords.
2006-05-11 Paul Emsley <emsley@ysbl.york.ac.uk>
* coords/Bond_lines.cc: (construct_from_asc): Added in cross-bonds
to hydrogens that don't have bonds. Blasted hydrogens will no
longer seem to disappear.
2006-05-10 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.h: ghost_molecule_display_t, cleaned up
usage of display_it_flag [valgrind was complaining [rightly]].
2006-05-09 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (set_show_unit_cells_all): Check maps too!
[PRE].
* src/callbacks.c (on_unit_cell_no_radiobutton_toggled): unit cell
radio button callbacks added. Now these radio button pair has
immediate effect [PRE].
2006-04-25 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc: (add_typed_pointer_atom): Set
attributes correctly for user-typed pointer atom.
2006-04-24 Paul Emsley <emsley@ysbl.york.ac.uk>
* ligand/Makefile.am: Use libcoot-ligand.la throughout.
2006-04-24 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/rama_plot.cc: (draw_2_phi_psi_sets_on_canvas): remove bad
shadowing of loop variable. [FR].
* src/molecule-class-info-other.cc: proper syntax for
coot::nomenclature [remove extra qualification] [FR].
* src/molecule-class-info-ncs.cc: make
copy_residue_range_using_from_ncs_master_to_other_using_ghost()
return a value [FR].
2006-04-19 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (set_graphics_window_size) add
use_graphics_interface_flag protection.
2006-04-17 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface-info.cc: (place_text), (remove_text) Added
fuctions. Add 3-d text [the text doesn't rotate, it stays
readable].
* src/c-interface.cc: Created function get_monomer() from the
internals of handle_get_libcheck_monomer_code(). get_monomer()
can be used from the scripting layer.
* src/c-interface.cc (safe-scheme-command). Now returns a value,
SCM, which can be decoded in the calling function. A good thing.
[This means that libguile.h had to be included in c-interface.h].
2006-04-15 Paul Emsley <emsley@ysbl.york.ac.uk>
* coot-utils/peak-search.hh (coot): remove extra qualification for
find_protein_to_origin_translations() [test compile with 4.1.0].
2006-04-14 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.h: remove molecule_class_info_t from
function declaration for change_chain_id_with_residue_range [DB].
* src/rama_plot.hh: remove coot::rama_plot:: from function
declaration for get_phi_psi [DB].
* coot-utils/coot-map-heavy.hh (ffear_search): remove class
component of function name for
filter_by_distance_to_higher_peak() [also DB].
* coords/Cartesian.h: add proper declaration of friend functions.
Ancient broken code (however did it compile before?)! Compilation
problem spotted Donnie Berkholz.
2006-04-12 Paul Emsley <emsley@localhost>
* src/molecule-class-info-mutate.cc (mutate_base_internal): Allow
Ud and Tr as possible bases from which to mutate.
2006-04-13 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* ligand/wiggly-ligand.cc: Added #include for coot-utils.hh, it
seems to be needed in the case where GSL is not defined? Anyway,
no harm in explicitly including it.
2006-04-11 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/graphics-info-navigation.cc: (fill_go_to_atom_residue_list):
make the 2000 residue item limit change to 20000. Now the widget
behaviour is different, but you can exapand chains past the G
chain [the 2000th residue] individually. This is better, I suppose.
2006-04-11 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info.cc: (apply_undo): Update the ramachandran plot
[if it exists for this molecule].
* coot-utils/coot-utils.cc: (create_directory): moved body of
make_directory_maybe here and changed logic of fstat vs is_dir
tests so that we don't test for a directory before file exists.
2006-04-04 Paul Emsley <emsley@ysbl.york.ac.uk>
Release 0.1
* src/graphics-info-modelling.cc:
(new_alt_conf_occ_adjustment_changed): Don't change the alt conf
for fully occupied atoms.
2006-04-03 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/callbacks.c (on_rotate_translate_obj_cancel_button_clicked):
COOT_ROTATE_TRANSLATE_DIALOG remembers where it was put when we
press the Cancel button.
2006-04-01 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface-build.cc (delete_residue_range): check the
status of the "Keep Active" dialog before trying to close the
dialog. Bug reported by Bernhard Lohkamp.
2006-03-30 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/c-interface-waters.cc (renumber_waters): function added
* src/molecule-class-info-other.cc (renumber_waters): function
added.
* src/c-interface.cc: (auto_read_make_and_draw_maps): if "FWT",
"DELFWT" column labels fail, try "2FOFCWT" and "FOFCWT" also.
* src/rama_plot.cc: created function phi_psi_pair_helper_t
make_phi_psi_pair() which is the engine for making phi/psi pairs
from 2 chains. Uses new utility function std::pair<short int,
coot::phi_psi_t> get_phi_psi().
The GUI menu item has been renamed to "Kleywegt Plot" as per
conversation with George Sheldrick.
2006-02-26 Paul Emsley <emsley@ysbl.york.ac.uk>
* ligand/Makefile.am (test_fffear_in_coot_LDADD): Add coot-compat
to get the correct getopt_long() as suggested by Ezra.
* src/main.cc and cmtz-cinterface.cc: Patch as Ezra suggests
commenting out NLS code.
2005-12-02 Paul Emsley <emsley@ysbl.york.ac.uk>
* coords/Bond_lines.cc: (do_colour_by_chain_bonds) and
(do_colour_by_molecule_bonds): both now look at the atom element
and draw_hydrogens_flag. Also removed atom selection indexing and
just just atom pointers (which should be propogated to other
functions in this class).
2005-12-01 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (apply_bond_parameters): remove looking for
the "carbons only" checkbuton.
2005-11-30 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc:
(initialize_coordinate_things_on_read_molecule_internal): add
setting of the [initial] bond colour map rotation step and "doit"
flag.
2005-11-12 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info.cc: (insert_coords_chage_altconf) and
(insert_coords_atoms_into_residue_internal): Add shelx occupancy.
-1 is used when this is not from a shelx file.
* coot-utils/coot-shelx-ins.cc: Add add_fvar function which added
a free variable and returns the index of the new free variable
* coords/mmdb.cc: (get_atom_selection): added ifdefs for
HAVE_MMDB_IGNORE_HASH. May need to sort this out by hand.
2005-11-11 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/molecule-class-info-widget-work.cc:
(ncs_control_change_ncs_master_to_chain_update_widget): created.
When we change the NCS master the toggle buttons for the displayed
ghost chains need to change too.
2005-11-10 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/cmtz-interface.cc: (get_f_phi_columns): use try/catch
mechanism to stop crash on trying to CCP4MTZfile::open_read a cif
file.
2005-11-06 Paul Emsley <emsley@ysbl.york.ac.uk>
* The move to CCP4 distribution of fftw, cmtz, cmap, mmdb, ssm,
clipper libraries. Substantial changes not documented here.
This diff is 38,000 lines.
mmtz and mmtz-extras have gone. New clipper-based mtz looking
routine added (cmtz-interface.cc).
Crystal and dataset info now appear in the mtz column chooser and
this had to be accounted for, so much splitting and recombining of
strings (new functions added).
macros updates to match ccp4 placing of include files.
The autobuilder is updated.
2005-11-05 Paul Emsley <emsley@ysbl.york.ac.uk>
* geometry/protein-geometry-mmdb.cc (comp_atom_pad_atom_name): I
was getting the atom name wrong for "CCB" with element "C", so now
a check is made to see if first letter is the element name.
2005-10-31 Paul Emsley <emsley@ysbl.york.ac.uk>
* macros/with-guile.m4, macros/with-python.m4: applied Ezra's
patch to use AM_CONDITIONAL to get to the wrapped guile interface.
2005-10-30 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/c-interface.cc: (handle_read_draw_molecule_with_recentre):
add statusbar text when the molecule fails to read.
2005-10-29 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/globjects.cc (key_press_event): add call to new scheme
function graphics-general-key-press-hook for as yet undefined
keys [Bryan Lepore].
2005-10-19 Paul Emsley <emsley@localhost>
* src/c-interface.cc: (another_level_from_map_molecule_number):
only try to mess with the contor levels of molecule istat if istat
is not an error [-1, e.g. from map, not mtz file]. Fixes
another-level crash.
2005-10-18 Paul Emsley <emsley@localhost>
* coot-utils/coot-fffear.cc: file created. For fffear class,
moved out of coot-map-heavy.cc
* coot-utils/coot-coord-utils.cc (pad_atom_name): copied from
geometry class. Should rationalize at some stage.
* coot-utils/coot-shelx-ins.cc: (make_atom_name): new version
which uses atom element and calls new util function
pad_atom_name().
2005-10-16 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/graphics-info.cc: (drag_refine_refine_intermediate_atoms):
created. Function for Frank von Delft.
* src/globjects.cc: (glarea_motion_notify): if dragged refinement
intermediate refinement set then refine intermediate atoms.
* src/molecule-class-info-other.cc: (add_OXT_to_residue): instead
of finding total 4 atoms, check that each of them has been
found. Now we can add OXT to residues with an alt conf.
2005-10-04 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info-pick.cc
(rotate_intermediate_atoms_round_screen_x): function created.
Called by rotate_intermediate_atoms_maybe().
* src/globjects.cc: (glarea_motion_notify):
rotate_intermediate_atoms_maybe() now has axis argument and uses y
diff for rotation round the screen X axis.
2005-09-23 Paul Emsley <emsley@ysbl.york.ac.uk>
* src/graphics-info-state.cc: (save-state_command): If
contoured_by_sigma_p() I meant to push back command strings, not
display strings. Fixes saving contour state issue for Bob Nolte.
* src/graphics-info-graphs.cc: (rotamers_from_mol): use dunbrack
constructor that adds extra PHE/TYR.
2005-09-20 Paul Emsley <emsley@ysbl.york.ac.uk>
* coot-utils/peak-search.cc: (get_peaks): don't move the negative
cluster centres to local peak.
* ligand/ligand.cc: (fit_ligand_to_cluster): Try each orientation
eigen. Changed [created a version with extra args of the eigen
ori] of transform_ligand_atom() and fit_ligand_copy().
(calculate_cluster_centres_and_eigens): After sorting the eigen
values, check the matrix determinant. If negative, swap axes 2
and 3. No longer inverts [chiral] ligands.
* coot-utils/peak-search.cc: (get_peaks): Don't used
move_grid_to_peak on cluster centres of negative peaks.
2005-09-19 Paul Emsley <emsley@ysbl.york.ac.uk>
* coords/Bond_lines.cc: (handle_MET_or_MSE_case): Add alt conf
testing to bonds. Also changed CYS case.
* ligand/ligand-extras.cc: (fit_water_internal): major rewrite.
Now uses list for clusters rather than vector. We only calculate
clusters once. Sphericity test has been removed.
2005-09-16 Paul Emsley <emsley@ysbl.york.ac.uk>
* ideal/simple-restraint.cc: (make_link_restraints): test for
neighbouring residues [by residue seq number]. Fixes problem of
refining next to residue with all atoms in alt confs.
* src/molecule-class-info-other.cc:
(do_180_degree_side_chain_flip): make the alt conf work by using a
residue copy.
2005-09-15 Paul Emsley <emsley@ysbl.york.ac.uk>
* geometry/protein-geometry.cc: (try_dynamic_add): Add in logic to
try to find "XXX-b-D.cif" or "XXX-a-L.cif"
* ideal/simple-restraint.cc: (find_link_type): override the return
value of find_glycosidic_linkage_type() until
find_glycosidic_linkage_type() returns sensible result. Fixing
flying carbohydrate.
2005-09-12 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/molecule-class-info-other.cc: (make_ball_and_stick): put the
glMaterialfv() call for specular inside the bond loop to colour
for bond type and comment out GL_AMBIENT_AND_DIFFUSE and
GL_EMISSION [no idea why they were there - not clear thinking...].
Ball and stick looks good now. I need to be able to remove the
object at some stage.
2005-09-11 Paul Emsley <paulemsley@ysbl.york.ac.uk>
* src/graphics-info-defines.cc:
(other_modelling_tools_toggle_button_name_list): correct name of
cis/trans button.
* ligand/residue_by_phi_psi.cc: extract function
build_C_terminal_ALA() and build_N_terminal_ALA() out of
residue_by_phi_psi class [from
construct_prev_res_from_rama_angles() and
construct_next_res_from_rama_angles()].
* ligand/helix-placement.cc: (build_on_N_end, build_on_C_end,
trim_end, build_N_terminal_ALA, build_C_terminal_ALA): created to
extend or trim the placed helix.