


------


   o Does is_mainchain_atom() working for mainchain hydrogens?  
     You mean is_main_chain_p().  Yes it is.
     ::: 1

   o need (residues-near-point imol radius) function.  ::: 1

* Done.  With test.  Needs python version filled.

   o Dynamic distances define need a pick cursor. ::: 1

* Easy.  Done 

   o rotamer-score function needs to be filled ::: 1

* Done.  Added test.

   o Move widget functions in c-interface-build.cc to
     c-interface-gui.cc (or consider new c-interface-build-gui.cc). ::: 1

* Done with the c-interface-build-gui.cc option.

   o Give the user a chance to edit the ins file before it is sent off
     for refinement [Tobias Beck].  Not doing so, as currently,
     practically makes the shelxl refine in Coot useless if the user
     needs to modify the file.  Fire up a text widget with the .ins file
     in it.  ::: 2

* Done.  Quite easy.

   o Rotamer plots need to update on multiple do/undos. ::: 1

* Done. Easy - just call update_geometry_graphs() with an asc on
  apply_undo().

   o enable --splash-screen  ::: 1

* Easy.  Create a function, added to the bottom of gtk-manual.cc.
  Tricky thing was to edit support.c to check this directory and
  absolute path name.  Will the changes to support.c remain intact?
  Or does support.c get overwritten?  Maybe, on using post-glade.  OK,
  I have turned off the writing of support files in glade.

   o Consider setting the "handled" flag only for key pressed that did
     something, e.g. we could then use the "B" and "S" keys, because they
     are not often used.  Maybe "A" too. ::: 1

* Done.

   o The lib dir should be set with AC_CHECK_LIB, not just "lib". Tim
     Fenn. ::: 2
 
* Let's hear from Tim Fenn.  OK, he replied.  Non-trivial. 
  OK, done I think.  I used AC_LIB_PREPARE_MULTILIB and $acl_libdirstem.
  I am presuming that does what he wanted.  On re-reading, perhaps
  not (but only perhaps).

   o add a mechanism where we can register functions to run after
     refinement and/or regularization. 
  
     or deleting things says JED.  In fact, a funtion to run that is
      attached to a molecule (somehow) on any
      update/change/manipulation. ::: 2

* Done for scm, I added manipulation-modes.hh so that the
  MOVINGATOMS, DELETED and MUTATED variables were available from
  scheme, (an _ in MOVING_ATOMS means that fails to be exported).

   o colour by B-factor CA mode, (CA + Ligs atom sel should be used
     for B-factor colouring mode).  Don't forget picking
     (grphics-info-pick c.f. CA_BONDS_PLUS_LIGANDS_SEC_STRUCT_COLOUR)
     ::: 1

* Done.


   o Use write_connectivity to generate ligand hydrogens. Use reduce
     and probe to make ligand interactions. It might be needed to ask
     Eugene about this.  Typical example is I have a model/PDB of
     protein and a model/PDB that has CONECT cards (written by
     write-connectivity and then appened to the PDB file).  I want to
     merge ligand with its connectivity to the protein molecule.  Or
     generate the connectivity and add it directly to the ligand
     molecule without going via a file and file append.

     I went for the separate file and append option with goosh-command
     and cat.  Works nicely. 
     ::: 1

* Well, that it works nicely was nothing to do with me, as it turns
  out, and everything to do with new probe (I suppose).  I doesn't
  need CONECT cards to do the ligand hydrogen contacts now.


   o need a function (bound to Shift D) to update dots centred around
     this point.  interactive-probe does something like we want, but
     with the filenames already written to disk.  We need to protect
     interactive-probe by checking a global flag that is set the
     first time we run interactive-probe (i.e. we test for
     command-in-path? only once) ::: 1

* This turned out to be much harder that I'd supposed.  First, I
  needed to turn off the Shifted key bindings (now D is different to
  d).  Next, I had to write a new routine probe-local-sphere which
  uses get-probe-dots-from.  There was a problem because if the atom
  selection radius and the probe radius are the same, then sometimes
  the middle atom of a bonded angle set is missing (outside the
  sphere) and that leads to bad clashes.  So I had to update
  new-molecule-by-sphere-selection to allow the writing of whole
  residues optionally.  This prevents the missing middle atom problem
  and now the probe-local-sphere works nicely. There is a problem of
  alt confs here though.  The alt conf specifier in
  deep_copy_this_residue() is checked "by hand" so "*" doesn't work.
  Maybe deep_copy_this_residue() [mmdb-extras, I think] should be
  changed so that it does.


   o Display ligand diapoles using charges from cif file. ::: 4

* There was a problem in orienting the dipole arrow.  Talk with Kevin
  fixed that.  I needed a dummy point to fill the rotation matrix.


   o Why does NAG not refine? e.g. 1h4p. ::: 2
     
* Actually it refines fine.  The problem is that 1h4p has residues out
  of order which mess up the residue selection. Let's add a function
  that test if residues are number in increasing order for a
  particular chain.  Let's use that function and if they are not in
  order, then add that to the warning text of the
  no_restraints_dialog.  OK, needs testing on a PDB file that has an
  unknown monomer but residues are not out of order.  OK, tested. Fine.


   o geometry graph for residues at a gap - makes an inappropriate
     link - e.g. 45-47 - it should check by distance.  Make sure that
     a gap between a refined residue and a flank is handled properly
     (i.e. there should be no flanking restraints in that direction).
     ::: 1 [JED]

* Seems good now (including flanking refine). 20080112.

   o find-waters --mapin 3bwp.map ... fails to run (silently) but
     using --hklin, --f and --phi worked. ::: 1

* Done.  'if' logic messed up. 20080112.

   o reset view behaves strangely sometimes? ::: 1

* Done.  A fixed value was being used in
  setRotationCentreAndZoom(). 20080112

   o Add a test for clear of generic object. ::: 1

* Done.  There was a bug in indexing of the generic object
  array. 20080112

   o Art authors: 
       world in connect-to-world is "cartoon globe" by lunanaut
       computer mouse for scroll wheel by crispy.

* Done.

   o write_residue_range_to_pdb_file need to write the correct chain
     ::: 1

* Done.

   o Refine CL - should behave sensibly - possibly looking at
     neighbours e.g. sphere refine ::: 2

* Done.

   o Add terminal residue does not respect the default B factor [Pete
     Meyer] ::: 1

   o add the ability to turn off shadows in raster3d output ::: 1

* Done.

   o displaying additional representations turns symmetry equivalent
     atoms into fat bonds. [JED] ::: 1

* Done.

   o Add a GUI for mutate-by-overlap acting on active-residue.
     Simple, use generic-single-entry ::: 1

* Done for scm.

   o Make it more clear that the SMILES interface uses libcheck.
     (perhaps grey out the function if libcheck is not available).
     ::: 1

* Done.

   o When a new residue is created (e.g. HOH) it should be checked
     against standard PDB residue types and if not found, then the
     atoms in the residue should be marked as HETATMs (set atom->Het).
     [ David Mathog noted problem]

     http://www.wwpdb.org/documentation/Format_v32_letter.pdf

     Consider hetify_residue_atoms_maybe(residue_p) which checks the
     residue name against standard pdb residue names, and if not
     there, then hetifies the atoms.

     Need to call this when reading the monomer-XXX.pdb output of
     libcheck.

     ::: 2

* Done.

   o A dipole for a selection of residues. Needs a test. ::: 2

* Done.

   o Check that sort chain ids does indeed sort the chain ids and does
     not change the order of the atoms in the molecule.  Convert to minimol 
     and sort the chains there - make sure that cell and symm are transfered.
     [Steven Sheriff, Bob Nolte] ::: 1

* Done.

   o sphere-refine in a region with undisplayed add-reps -> add reps
     displayed. ::: 1

* Done.  one liner: in update_additional_representations():
	 display_list_tags[handle].display_it = add_reps[i].show_it;


   o is -oldpdb in the input to reduce?

* It is now.

   o Rotate Translate: Add an additional GUI (possibly in the toolbar)
     to specify the type of R/T entity, a zone (default) a chain, a
     whole molecule. Include adding to the GUI the ability to swap
     rot_trans_object_type modes.  ::: 5

* Done.

   o Seg Ids (Mailing list issue):

      At least in these two situations, I think that COOT could make a
      very educated guess as to the correct SEGID.

       * In mutate (simple or otherwise), COOT could carry over what
         existed for the residue being mutated

       * In "insert after terminal residue" COOT could carry over what
         exists for the terminal residue

      These might not always be correct, but they should be 99+% of
      the time.

     Also mails from Phil Evans, Stephen Graham, Early April 2008
     about SEG ids.  Doing a NCS loop with Seg ids.  Doing a mutation
     with Segids (might be the same issue).  The segid for the new
     atoms should be inherited from those of the rest of the residue
     (if they are consistent). ::: 6

* mutate done (needs a test?).  But what about ncs-copy-residue-range? 
  Done, needs test. And what about add_terminal_residue, which uses
  NEW_COORDS_INSERT, I think.  It does. Coded, needs a test
  (set-atom-string-attribute now can take a "segid" tag), so we're 
  all set to make a test.  Done.


   o When you mutate an RNA base, it does it fine on the
     screen. However, when it writes out the file, it changes, e.g., Cr
     to Cd  [VR] ::: 1

* Done.  Test added.

   o Add user-define clicks ::: 1

* Done (Scheme version anyway)
   o Bill: This might be hard to implement, but in case it isn't, I
     thought it might be worth suggesting...

     It would be great to be able to click on a nucleotide base in a
     single strand of DNA or RNA and generate its W/C partner...  ::: 4
 
* Not so hard - generate a WC pair (just one base, double
  stranded). Fit the base atoms of one of those to the
  clicked-on-residue. Use the matrix to move the other residue.
  Bingo.  Needs atom-by-atom matching in the least-squares procedure -
  may need thinking about that. Bernhard mentioned that he would
  be looking at atom matching in lsq, so I will leave it for now.
  The base-pairing files are in ligand dir now.

  Done now.

   o Export the ligand fitting from a position (rather than searching
     the whole map to find cluster site). ::: 2

* Done.

   o redo sequence view ::: 10

* Done.  Maybe it will need enhancements later, but this is what I
  wanted to achieve for now.


   o crash: coot-download a structure 1ucs.  create a map from mtz,
     create another map from mtz (I meant to change the limits, but
     forgot). Delete that new map (using the button on display
     control). mtz read same mtz with reso limits -> crash.

 gtk_radio_button_set_group: assertion `!g_slist_find (group, radio_button)' failed

#0  0x034e2ce7 in gtk_radio_button_set_group () from /usr/lib/libgtk-x11-2.0.so.0
#1  0x034e2f61 in gtk_radio_button_new_with_label () from /usr/lib/libgtk-x11-2.0.so.0
#2  0x082e3bae in display_control_map_combo_box (display_control_window_glade=0x95e0cc0,
    name=0x8a035c4 "1ucs_sigmaa.mtz 2FOFCWT PH2FOFCWT 50.00  0.80", n=6) at ../../coot/src/gtk-manual.cc:1187
#3  0x0837219d in molecule_class_info_t::update_map_in_display_control_widget (this=0x9bafa30) at ../../coot/src/molecule-class-info-maps.cc:131
#4  0x0835a3cb in molecule_class_info_t::initialize_map_things_on_read_molecule (this=0x9bafa30, molecule_name=@0xbfb67fac,
    is_diff_map=-1078562068, swap_difference_map_colours=0) at ../../coot/src/molecule-class-info.cc:1250
#5  0x0837b39b in molecule_class_info_t::map_fill_from_mtz_with_reso_limits (this=0x9bafa30, mtz_file_name=@0xbfb68140, f_col=@0xbfb6813c,
    phi_col=@0xbfb68138, weight_col=@0xbfb68134, use_weights=0, is_anomalous_flag=0, is_diff_map=0, use_reso_limits=1, low_reso_limit=50,
    high_reso_limit=0.800000012, map_sampling_rate=1.5) at ../../coot/src/molecule-class-info-maps.cc:488
#6  0x0813e8f2 in make_and_draw_map_with_reso_with_refmac_params (
    mtz_file_name=0x9bdaa74 "/home/paule/Projects/build-coot-fc4-gtk2/src/coot-download/1ucs_sigmaa.mtz",
    f_col=0x9bf9b14 "/unknown/unknown221007/2FOFCWT", phi_col=0x9bf72c4 "/unknown/unknown221007/PH2FOFCWT", weight_col=0x84d9204 "", use_weights=0,
    is_diff_map=0, have_refmac_params=0, fobs_col=0x84d9204 "", sigfobs_col=0x84d9204 "", r_free_col=0x84d9204 "", sensible_r_free_col=0,
    is_anomalous_flag=0, use_reso_limits=1, low_reso_limit=50, high_reso_limit=0.800000012) at ../../coot/src/c-interface.cc:1131
#7  0x0815508c in handle_column_label_make_fourier (column_label_window=0x9c21060) at ../../coot/src/c-interface-gui.cc:364

and again, similar, this time I shut and open the dialog (not sure if
I deleted after I opened again though).

#0  0x034e2ce7 in gtk_radio_button_set_group () from /usr/lib/libgtk-x11-2.0.so.0
#1  0x034e2f61 in gtk_radio_button_new_with_label () from /usr/lib/libgtk-x11-2.0.so.0
#2  0x082e38ca in display_control_map_combo_box (display_control_window_glade=0x9855550,
    name=0x987df5c "1ucs_sigmaa.mtz 2FOFCWT PH2FOFCWT 50.00  1.20", n=5) at ../../coot/src/gtk-manual.cc:1187
#3  0x08371ec9 in molecule_class_info_t::update_map_in_display_control_widget (this=0x9e98c58) at ../../coot/src/molecule-class-info-maps.cc:131
#4  0x0835a0f7 in molecule_class_info_t::initialize_map_things_on_read_molecule (this=0x9e98c58, molecule_name=@0xbfb254ac,
    is_diff_map=-1078835220, swap_difference_map_colours=0) at ../../coot/src/molecule-class-info.cc:1250
#5  0x0837b0c7 in molecule_class_info_t::map_fill_from_mtz_with_reso_limits (this=0x9e98c58, mtz_file_name=@0xbfb25640, f_col=@0xbfb2563c,
    phi_col=@0xbfb25638, weight_col=@0xbfb25634, use_weights=0, is_anomalous_flag=0, is_diff_map=0, use_reso_limits=1, low_reso_limit=50,
    high_reso_limit=1.20000005, map_sampling_rate=5) at ../../coot/src/molecule-class-info-maps.cc:488
#6  0x0813e8fe in make_and_draw_map_with_reso_with_refmac_params (
    mtz_file_name=0x987f6c4 "/home/paule/Projects/build-coot-fc4-gtk2/src/coot-download/1ucs_sigmaa.mtz",
    f_col=0x9876fe4 "/unknown/unknown221007/2FOFCWT", phi_col=0x9872294 "/unknown/unknown221007/PH2FOFCWT", weight_col=0x84d8e84 "", use_weights=0,
    is_diff_map=0, have_refmac_params=0, fobs_col=0x84d8e84 "", sigfobs_col=0x84d8e84 "", r_free_col=0x84d8e84 "", sensible_r_free_col=0,
    is_anomalous_flag=0, use_reso_limits=1, low_reso_limit=50, high_reso_limit=1.20000005) at ../../coot/src/c-interface.cc:1131
#7  0x08155098 in handle_column_label_make_fourier (column_label_window=0x990f2e8) at ../../coot/src/c-interface-gui.cc:364


This time I think I did not delete the map using the display control
button, but I did use the Close molecule button!  Hmm!


#0  0x034e2ce7 in gtk_radio_button_set_group () from /usr/lib/libgtk-x11-2.0.so.0
#1  0x034e2f61 in gtk_radio_button_new_with_label () from /usr/lib/libgtk-x11-2.0.so.0
#2  0x082e38ca in display_control_map_combo_box (display_control_window_glade=0xa878b68,
    name=0xa8bff4c "1ucs_sigmaa.mtz 2FOFCWT PH2FOFCWT 50.00  1.80", n=5) at ../../coot/src/gtk-manual.cc:1187
#3  0x08371ec9 in molecule_class_info_t::update_map_in_display_control_widget (this=0xa97ac80) at ../../coot/src/molecule-class-info-maps.cc:131
#4  0x0835a0f7 in molecule_class_info_t::initialize_map_things_on_read_molecule (this=0xa97ac80, molecule_name=@0xbfae6e2c,
    is_diff_map=-1079090836, swap_difference_map_colours=0) at ../../coot/src/molecule-class-info.cc:1250
#5  0x0837b0c7 in molecule_class_info_t::map_fill_from_mtz_with_reso_limits (this=0xa97ac80, mtz_file_name=@0xbfae6fc0, f_col=@0xbfae6fbc,
    phi_col=@0xbfae6fb8, weight_col=@0xbfae6fb4, use_weights=0, is_anomalous_flag=0, is_diff_map=0, use_reso_limits=1, low_reso_limit=50,
    high_reso_limit=1.79999995, map_sampling_rate=5) at ../../coot/src/molecule-class-info-maps.cc:488
#6  0x0813e8fe in make_and_draw_map_with_reso_with_refmac_params (
    mtz_file_name=0xa88b9ac "/home/paule/Projects/build-coot-fc4-gtk2/src/coot-download/1ucs_sigmaa.mtz",
    f_col=0xa8b3fac "/unknown/unknown221007/2FOFCWT", phi_col=0xa8b8a74 "/unknown/unknown221007/PH2FOFCWT", weight_col=0x84d8e84 "", use_weights=0,
    is_diff_map=0, have_refmac_params=0, fobs_col=0x84d8e84 "", sigfobs_col=0x84d8e84 "", r_free_col=0x84d8e84 "", sensible_r_free_col=0,
    is_anomalous_flag=0, use_reso_limits=1, low_reso_limit=50, high_reso_limit=1.79999995) at ../../coot/src/c-interface.cc:1131
#7  0x08155098 in handle_column_label_make_fourier (column_label_window=0xa85e0e8) at ../../coot/src/c-interface-gui.cc:364

    ::: 2

* Fixed now that we don't handle the scroll group directly.

   o When reading in a dictionary twice, does it add or replace?  Why
     do I see 20 non-const non-H torsions in 3GP when using flexible
     ligands? ::: 2

* Done.
   o Check that ncs-chain-skip works for NCS heterodimer.  Use 3FCS.
     [Jianghai Zhu] ::: 1

   o "Fit ligand here" which gets a monomer then does a ligand search
     based on the blob at the current position. ::: 8

* I added a function to find a blob close to the given postion, then
  add it as a cluster.  That was fun. It made the cluster correctly,
  same as reference (blob 2).  Then trying to do wiggly ligands there
  I ran in to the problem.  I was wondering why I was getting a poor
  solution, the ribose was always rotated (compared to the reference
  and correct solution).  Why?  The torsion was wrong.  In the
  dictionary we have

 3GP      var_2    C8     N9     C1*    C2*      -78.375    2.000   1

  There is a torsion round N9 C1 - and in the wiggly ligand models it
  was always wrong.  It turns out that wiggly ligands was setting the
  torsion of the C8 N9 C1* H1* instead.  Hopelessly wrong.  To fix
  this needs a re-write of the torsion setting code. Sigh.  Strange
  that I haven't notice this before.  Waiting for Stuart to fix
  SetDihedralAngle().

* Done.  For now.


   o Crash [JED] 
Using host libthread_db library "/lib/tls/libthread_db.so.1".
Core was generated by `/apps/xtal/coot/current/linux/bin/coot-real'.
Program terminated with signal 11, Segmentation fault.
#0  safe_python_command_with_return (python_cmd=@0xbfffa5c0) at
c-interface.cc:5998
	in c-interface.cc
#0  safe_python_command_with_return (python_cmd=@0xbfffa5c0) at
c-interface.cc:5998
#1  0x082138c9 in graphics_info_t::run_post_manipulation_hook_py
(this=0xbfffa657, imol=3, mode=4) at graphics-info.cc:1112
#2  0x082135e3 in graphics_info_t::run_post_manipulation_hook
(this=0xbfffa657, imol=3, mode=4) at graphics-info.cc:1076
#3  0x082135b5 in graphics_info_t::accept_moving_atoms
(this=0xbfffa657) at graphics-info.cc:1066
#4  0x0814c261 in accept_regularizement () at c-interface-build.cc:4916
#5  0x085d426d in _wrap_accept_regularizement () at coot_wrap_guile.cc:14653
#6  0x400a430a in scm_deval () from
/apps/xtal/coot/current/linux/lib/libguile.so.12
#7  0x400a60e4 in scm_dapply () from
/apps/xtal/coot/current/linux/lib/libguile.so.12
#8  0x4009ee48 in scm_apply () from
/apps/xtal/coot/current/linux/lib/libguile.so.12

    This may be fixed now.  We fixed it when Bernhard came round after
    CCP4 dev meeting.

      ::: 1

   o Tobias Beck:

In /net/home/xtal/Building/coot/coot-Linux-i686-ubuntu-8.04.2-gtk1/share/guile/gtk-1.2/gtk.scm:
 127: 0* [apply #<procedure #f ()> ()]
In unknown file:
   ?: 1  [#<procedure #f ()>]
In /net/home/xtal/Building/coot/coot-Linux-i686-ubuntu-8.04.2-gtk1/share/coot/scheme/extensions.scm:
 625: 2  (let ((txt #) (imol #)) (if (number? imol) (if # # ...)) ...)
 628: 3* (if (number? imol) (if (= (string-length txt) 0) (shelxl-refine imol) ...))
 629: 4  (if (= (string-length txt) 0) (shelxl-refine imol) (shelxl-refine imol txt))
In /net/home/xtal/Building/coot/coot-Linux-i686-ubuntu-8.04.2-gtk1/share/coot/scheme/shelx.scm:
   ...
 145: 5  [shelxl-refine-inner 0 ...
/net/home/xtal/Building/coot/coot-Linux-i686-ubuntu-8.04.2-gtk1/share/coot/scheme/shelx.scm:145:7: While evaluating arguments to shelxl-refine-inner in expression (shelxl-refine-inner imol hkl-file-in-maybe ...):
/net/home/xtal/Building/coot/coot-Linux-i686-ubuntu-8.04.2-gtk1/share/coot/scheme/shelx.scm:145:7: Unbound variable: hkl-file-in-maybe 

    ::: 1

* Done.

   o Build with new mmdb 1.20.    ::: 1

* Done. 1.21 actually.



   o Crash from Joel Bard:
#0  on_background_white1_activate (menuitem=0x6e8e020, user_data=0x0)
    at callbacks.c:2028
#1  0x000000322120b16a in g_closure_invoke () from /lib64/libgobject-2.0.so.0
#2  0x000000322121b3bd in g_signal_override_class_closure ()
   from /lib64/libgobject-2.0.so.0
#3  0x000000322121c826 in g_signal_emit_valist ()
   from /lib64/libgobject-2.0.so.0
#4  0x000000322121ca03 in g_signal_emit () from /lib64/libgobject-2.0.so.0
#5  0x00002afe90a4716d in gtk_radio_menu_item_new_with_label_from_widget ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#6  0x000000322120b16a in g_closure_invoke () from /lib64/libgobject-2.0.so.0
#7  0x000000322121b80d in g_signal_override_class_closure ()
   from /lib64/libgobject-2.0.so.0
#8  0x000000322121c826 in g_signal_emit_valist ()
   from /lib64/libgobject-2.0.so.0
#9  0x000000322121ca03 in g_signal_emit () from /lib64/libgobject-2.0.so.0
#10 0x00000000005832d5 in on_background_colour1_activate (menuitem=0x6e8a580, 
    user_data=<value optimized out>) at callbacks.c:5853
#11 0x000000322120b16a in g_closure_invoke () from /lib64/libgobject-2.0.so.0
#12 0x000000322121b3bd in g_signal_override_class_closure ()
   from /lib64/libgobject-2.0.so.0
#13 0x000000322121c826 in g_signal_emit_valist ()
   from /lib64/libgobject-2.0.so.0
---Type <return> to continue, or q <return> to quit---
#14 0x000000322121ca03 in g_signal_emit () from /lib64/libgobject-2.0.so.0
#15 0x00002afe90b1445a in gtk_widget_activate ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#16 0x00002afe90a1fff1 in gtk_menu_shell_append ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#17 0x00002afe90a184e6 in gtk_menu_reorder_child ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#18 0x00002afe90a12fbd in gtk_marshal_BOOLEAN__VOID ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#19 0x000000322120b220 in g_closure_invoke () from /lib64/libgobject-2.0.so.0
#20 0x000000322121b9dd in g_signal_override_class_closure ()
   from /lib64/libgobject-2.0.so.0
#21 0x000000322121c5ef in g_signal_emit_valist ()
   from /lib64/libgobject-2.0.so.0
#22 0x000000322121ca03 in g_signal_emit () from /lib64/libgobject-2.0.so.0
#23 0x00002afe90b1078e in gtk_widget_get_default_style ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#24 0x00002afe90a12fbd in gtk_marshal_BOOLEAN__VOID ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#25 0x000000322120b16a in g_closure_invoke () from /lib64/libgobject-2.0.so.0
#26 0x000000322121b9dd in g_signal_override_class_closure ()
   from /lib64/libgobject-2.0.so.0
#27 0x000000322121c5ef in g_signal_emit_valist ()
---Type <return> to continue, or q <return> to quit---
   from /lib64/libgobject-2.0.so.0
#28 0x000000322121ca03 in g_signal_emit () from /lib64/libgobject-2.0.so.0
#29 0x00002afe90b1078e in gtk_widget_get_default_style ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#30 0x00002afe90a0d705 in gtk_main_do_event ()
   from /usr/lib64/libgtk-x11-2.0.so.0
#31 0x00000032236468cc in gdk_add_client_message_filter ()
   from /usr/lib64/libgdk-x11-2.0.so.0
#32 0x000000321fe2cf44 in g_main_context_dispatch ()
   from /lib64/libglib-2.0.so.0
#33 0x000000321fe2fd7d in g_main_context_check () from /lib64/libglib-2.0.so.0
#34 0x000000321fe3008a in g_main_loop_run () from /lib64/libglib-2.0.so.0
#35 0x00002afe90a0da53 in gtk_main () from /usr/lib64/libgtk-x11-2.0.so.0
#36 0x00000000004a344b in c_inner_main (closure=<value optimized out>, 
    argc=<value optimized out>, argv=0x7fff21675878) at c-inner-main.c:306
#37 0x00002afe8d2fdca6 in invoke_main_func ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#38 0x00002afe8d2d4a72 in c_body ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#39 0x00002afe8d339466 in scm_c_catch ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#40 0x00002afe8d2d4e12 in scm_i_with_continuation_barrier ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
---Type <return> to continue, or q <return> to quit---
#41 0x00002afe8d2d4eb0 in scm_c_with_continuation_barrier ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#42 0x00002afe8d338488 in scm_i_with_guile_and_parent ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#43 0x00002afe8d338514 in scm_with_guile ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#44 0x00002afe8d2fdc6b in scm_boot_guile ()
   from /d00/coot/bleeding_edge_coot/lib/libguile.so.17
#45 0x00000000004a2d73 in c_wrapper_scm_boot_guile (argc=115925024, argv=0x0)
    at c-inner-main.c:326
#46 0x000000000049978b in main (argc=3, argv=0x7fff21675878) at main.cc:569
Current language:  auto; currently c

     ::: 1

* anti-aliasing code re-worked.  I investigated, but couldn't see the
  cause of this.  Maybe I'll have to come back to it :(

   o Is the TER atoms remove from the "added-to-residue" on terminal
     residue addition?   ::: 1

* Yes it is.  Still have starred atoms though.

     o Steven Sheriff: fix up the difference map peaks so that I don't
       get two that are close together.  Done - test written.  Seems good, 
       needs a manual check. ::: 1

* Done.
    

     o  Wuyi> It supposed to ask for a pdb but nothing happened. I
        even loaded the pdb first. The coot 0.5.2 on Ubuntu works fine
        on same files.


> Wuyi Meng wrote:
>>
>> Hi Paul,
>>
>> I am having trouble to read phs file created from hkl2map. I am
>> running OSX 10.5.6 on an Intel MacBook Pro, both coot 0.6 pre or 0.5.2
>> have the error message:
>>
>> "
>>>>>>>>
>>>>>>>> CCP4 library signal mtz:File not identified as MTZ (Error)
>>
>>         raised in MtzGet <<<<<<
>> CCP4MTZfile: open_read - File missing or corrupted:
>> /Users/meng/tan/tan_i.phs
>> INFO:: not an mtz file: /Users/meng/tan/tan_i.phs
>>>>>>>>
>>>>>>>> CCP4 library signal mtz:File not identified as MTZ (Error)
>>
>>         raised in MtzGet <<<<<<
>> CCP4MTZfile: open_read - File missing or corrupted:
>> /Users/meng/tan/tan_i.phs
>> INFO:: not an mtz file: /Users/meng/tan/tan_i.phs
>> INFO:: data file /Users/meng/tan/tan_i.phs is not a valid mtz file
>> /Users/meng/tan/tan_i.phs is a .phs file
>> " 

      ::: 2 

* Fixed.  I did nothing.  User updated, maybe Bill fixed it.

   o sequence view fails to start at the correct residue when using
    chains starting at 120, 150 or so?] Use offset-resno-test.pdb
    ::: 2
   
* Done.

     o Steven Sheriff:

        In v0.5.2 and earlier (at least back to v0.3 something or
        other), when one adds water molecules in the vicinity of one
        another Measures->Environment Distance... usually does not
        pick up the distances between newly added water molecules
        (unfortunately, I don't think this is a 100% failure, which,
        of course, will make it much more difficult to debug).

      ::: 1

* Done - worked around a seqDist problem (mmdb bug) in SeekContacts().


   o make reading a dirty cif file report the bad line number. ::: 1

* It seems that that this was already in place.

   o Reading in a map messes with the scroll button in the display
     menu (possibly). JED.
    ::: 1 

* Fixed.


   o JED: File -> Coordinates, resize window big. Cancel File ->
     Coordinates, resize window to small -> Fail.  ::: 1

* Done. Use gtk_window_set_default_size() not gtk_widget_set_size_request().


   o documetation for Torsion General. ::: 0.3
   You need to click on the torsion-general icon, then click 4 atoms
   that describe the torsion - the first atom will be the base (non
   moving) part of the atom tree, on clicking the 4th atom a dialog
   will pop up with a "Reverse" button [1].  Move this dialog out of
   the way and then left mouse click and drag in the main window will
   rotate the "top" part of the residue round the clicked atoms 2 and
   3.  When you are happy, click "Accept".


    o An interface to make dotted lines (generic objects).  Tobias Beck ::: 1

* Done.  It was easy.  Reduce to 1 point.

   o Ramachandran Plots need a molecule name/number title [Wendy
     Offen] ::: 1

* Done - a while ago.

   o crash when adding a view annoation (first I added an annotation
     to view 4 (which didn't exist))   ::: 1

* Done - a while ago also.


   o (reorder-chains 0) -> 

     bad atom (occ b element expression) 
     object: (1.0 17.4099998474121 " C" "")
     etc...
     ::: 1

* Done - using scm_is_string().  Not sure if this is in 1.6.

   o When starting up with --no-state-script, don't write a state
     script on closing.  ::: 0.5

* Done.

   o > I was wondering if there's a way to avoid that a new "symmetry
       controller" window opens every time I click on the "symmetry by
       molecule..." button of the "Show symmetry?" dialog, rather than
       just bringing to the front an already opened one.
                                         Sebastiano Pasqualato  ::: 1


* Done.

   o normal usage (the start up script doesn't seem to be the issue)
** (lt-coot-real:1937): WARNING **: Widget not found: map_scroll_button_3
   This happens on opening the Display Manager (with 2 maps (2 and 3)
   and 2 pdbs (0 and 1).  (but also I'd done (pointer-atom-molecule)
   but (molecule-number-list was (0 1 2 3)), so that is probably not
   relevant.)
    ::: 1

    o On map masking, on pressing the "Mask" button with inversion enabled:

** (lt-coot-real:9413): WARNING **: Widget not found: map_scroll_button_3
changed active state to #t
debug:: invert-mask? is #t
INFO:: Masking around 0 atoms

Elsewhere: 

** (lt-coot-real:5745): WARNING **: Widget not found: map_scroll_button_4

** (lt-coot-real:5745): WARNING **: Widget not found: map_scroll_button_5

** (lt-coot-real:5745): WARNING **: Widget not found: map_scroll_button_4

** (lt-coot-real:5745): WARNING **: Widget not found: map_scroll_button_5

** (lt-coot-real:5745): WARNING **: Widget not found: map_scroll_button_5

             ::: 1

 * Done.  It was get_radio_button_in_scroll_group() looking for
   map_scroll_button buttons that did not yet exist.


   o put density-score-by-residue into distro tar file
     Done.  Needs checking. ::: 1


* It certainly did need checking.  On bubbles the previous binary
  density-score-by-residue was added to the source tar file instead of
  the script in the source src dir.


  
   o Remove debugging:
     DEBUG:: on ok button pressed, active index 0

* Done - callbacks.c

   o fix-nomenclature-errors added to GUI ::: 1

* Done.


   o Ingo K.: try to pepflip a peptide with alt conf "B" - it flips
     the "A" version.  ::: 1

* Done.  Big rewrite of pepflip and small rewrite of get-atom.


   o Time Grune: When you read in a shelx ins file, it ignores the
     "Recentre" check button on the file selection dialog.  ::: 1

* Done.


   o Investigate interupting long fitting/Post MR tools [JED request] 
     Add a stop button to the toolbar perhaps.
     ::: 2

* gtk-toolbar-insert and gtk-toolbutton-new are not available in
  guile-gtk-2.0, or so it currently seems to me.  This can't be done
  from scripting then. Hmm... [Probably possible in python].  Does
  this mean I should consider looking at guile-gnome?  Or how about
  coot-add-main-toolbar-stop-toolbutton which gets passed a function
  to call when the button is clicked.  Need to think about how the
  button goes away without being clicked.  Pass back the widget?
  Seems complex - how about just destroy-toolbar-stop-toolbutton. Yes.
  Should those refinement scripts be run as idle functions then?  

  Done, at least in scheme.

   o Tim Gruene: When you add a terminal residue to a .ins molecule,
     then the main chain atoms have occupancy 1.0.  ::: 1

   o Refining a GLC gives:

There are 2 data in /home/paule/autobuild/Linux-kalypso-pre-release-gtk2/share/coot/lib/data/monomers/g/GLC-b-D.cif
WARNING: residue type GLC not found in restraints dictionary (chiral)
There are 2 data in /home/paule/autobuild/Linux-kalypso-pre-release-gtk2/share/coot/lib/data/monomers/g/GLC-b-D.cif
WARNING: residue type GLC not found in restraints dictionary (chiral)
There are 2 data in /home/paule/autobuild/Linux-kalypso-pre-release-gtk2/share/coot/lib/data/monomers/g/GLC-b-D.cif
WARNING: residue type GLC not found in restraints dictionary (chiral)
There are 2 data in /home/paule/autobuild/Linux-kalypso-pre-release-gtk2/share/coot/lib/data/monomers/g/GLC-b-D.cif
WARNING: residue type GLC not found in restraints dictionary (chiral)
c-interface clear_up_moving_atoms...   
     ::: 2


   o What happened to WC partner (watson_crick_pair())? Other Modelling Tools "Base Pair"
    ::: 0.2
 
*  Other Modelling Tools.


   o Add cancel button to rama refine ::: 1

* Done.


   o Rama-refine rnase: Does it work properly?  (possibly more work
     here.) ::: 1

* It's fine.



   o Look at 1y7l difference map. Peaks 12 and 13 are too close to
     each other? 1.12A. ::: 1 

* max_closeness was 1.0.  I changed it to 2.0

   o CA+Ligands has gone into CA by B-factor mode.  Don't like - it 
     should be just the same as CA mode. There is a mix up over what
     bond_colour_type means. ::: 1  

* Bernhard quick-fixed - rev 1918.



   o centos build crash:

   1. 0.6-pre-1 (revision 2061) [with guile 1.8.6 embedded] [with
   python 2.6.0 embedded]

   Using host libthread_db library "/lib/tls/libthread_db.so.1".
   Core was generated by
   `/x/coot-Linux-i386-centos-4-gtk2-python/bin/coot-real'.
   Program terminated with signal 11, Segmentation fault.
   #0  0x40a4b3ea in gtk_widget_ref () from /usr/lib/libgtk-x11-2.0.so.0
   #0  0x40a4b3ea in gtk_widget_ref () from /usr/lib/libgtk-x11-2.0.so.0
   #1  0x082db532 in create_window1 () at gtk2-interface.c:2607
   #2  0x08106ea7 in main (argc=1, argv=0xbfe30334) at main.cc:264

   1962 runs just fine.

   ::: 1 

* Fixed.


   o Go To Atom residue tree does not update properly (JED)
   Do this:
   - read in a pdb file
   - open the go to atom window
   - read in another pdb file (with different chains etc)
   - try to set the go to atom molecule in the dropdown to the new one
   -> the chain/atom tree won't update, only on multiple changing back
      and forth between go to atom molecules. 
   ::: 1

* Done.

   o Move Koala to gcc 4.1.2 20080704 (RH 4.1.2-44) or better.  See
     Esser build log problems.  ::: 2

* Fixed, well Lothar has it building.


   o Some tests for rigid body fitting many residue.  Consider
     residues with TERs and alt confs. [Bob Nolte] ::: 2 

* I did it by hand.  TERs are excluded in construction of a minimol
  molecule from a CMMDBManager now.  rigid body fitting an alt conf
  seems fine.


   o Job for Bernie?  Tool bar in text mode does not show text for 
     the new rotate/translate toolbar menu button.

* Done (in glade-2)


   o Document the post-manipulation-hook.  How, for example, might you
     use it to move the residue added on a "Add Terminal residue"? 
     [Ethan Merritt] ::: 1

* Done.

   o Move Koala to gcc 4.1.2 20080704 (RH 4.1.2-44) or better.  See
     Esser build log problems.  ::: 2

* Not fully done, but Lothar can build coot now.


   o Add terminal residue has disconnected atoms.  Why? This is an
     extremely deeply-buried problem. ::: 4

 * Done by Bernhard (and Eugene).

   o Fix Pukka Puckers ::: 4

* Done.

   o Tweak the go-to-blob algorithm to much favour blobs at the front.
     Especially those above the displayed contour level. Does this
     work with the refinement map?  What happens when the refinement
     map is not defined?  ::: 1

* Done.


   o Integrate scripting functions into main documentation somehow.
     Well, you can look at this, if it is hard, punt it.  
     ::: 3

* It looks like it can be done using @html, @end html stripping out the
  body etc tags. Ugly though.  Include files need to be in source doc
  directory.  Call it xxx.html.texi and add @html tags in there.

  Actually, there is a better way, use the JED conversion script.

  Done.  At last.  What an effort.


   o Backrub-based auto-fit rotamer search.  Question: how do I test
     this? Synthetic map?  How does it work when we do this for an alt
     conf too?  ::: 5

* Done.  Actually quite easy.


   o get-monomer fails for JED.  Why? ::: 1

* It apparently no longer does.  Yeay.


   o multiple residue ranges, glycosylation, covalent bond entities,
     make sure it works with alt confs and residues with TER atoms.  

     Sphere refinement on N-linked NAG glycans work fine (e.g. 1pp4).

     OK, sphere refinement on a residue next to a residue with an alt
     conf fails (E_NOPROGRESS).  

     Sphere refinement on a resiude with an alt conf ignores the
     centre residue and refines the residues around it). Hard.

     ::: 10

* What else is there to do here?  Write a test.

   o File differences mentioned by Bill?  

* Not need now


   o Why is the brief text for have_unsaved_changes_p() not showing in
     the on-line documentation?  ::: 0.5

* Because it was including the wrong file.

   o Distances should undisplay when the molecule to which they relate
   (either of them) is undisplayed.  ::: 1 

* Done.


   o symmetry molecule by symop.  Check that pre_shift_to_origin_abc
     is applied the right way (currently I think that it is not (not
     at least with the new-molecule-by-symop usage in
     extensions)). ::: 1

* Seems OK now.


   o Move "Add strand here" next to "add Helix here" ::: 0.5

* Done.

   o Fix this: 

** (coot-real:16099): WARNING **: Widget not found: preferences_font_size_small_radionbutton

(coot-real:16099): Gtk-CRITICAL **: gtk_toggle_button_set_active: assertion `GTK_IS_TOGGLE_BUTTON (toggle_button)' failed

    ::: 0.5

* Done.  typo.


   o What about if there are python and scheme bindings to a
     particular key?  graphics-general-key-press-hook should return the
     status of the key being found and the binding function used.  Then
     if not, we can run the python function [JED]. ::: 0.5

* No, I am not going to do that, key bindings are either all python or all scheme.

   o Make sure that .coot.py keybindings appear in the keybindings
     GUI. Get Python working first. Hmm. ::: 0.1

* No.

   o Geometric distortions graph for alt confs - currently broken? ::: 1
 
* Can't find it if it is.


   o Environment distances should go off when the molecule to which
     the relate is undisplayed. ::: 1

* Done.


   o pir sequence assignment should overwrite the seqence (if
     possible) not add to the sequences.  
     ::: 1

* Done.

   o Regularize monomer-3GP. Turn on torsion angle restraints.
     Regularize again. Look at above var_2 torsion.  After
     minimization, torsion is 171.09 degrees.  Wrong.  The minimizer
     doesn't terminate though. Use libcheck_3GP-torsion-filtered.cif 

     20090723 on trying again torsion is -115.  [Target is -78].
     Still doesn't terminate properly though.
     chisq torsions: 45.3986 Hmm.

     On using torsion in refinement and using just the N9-C1 torsion,
     and 6 or so rounds, it terminates correctly.  However, torsion is
     -157.9 and chi-sq 24.6.

     ::: 4

* Fixed.  It was a circular symmetry bug.


   o JED data mmCIF data file, scroll button is wrong ::: 1

* Done.


   o Communication with PISA.  Get PISA on jackal.  I'd like show the
     interface with molprobity dots.  pisa-interaction ::: 8


* Done.  Well pisa-interaction (which is interfaces) not done
  properly, but what I have (the assemblies interface) I like now.
  Could do with more feedback, perhaps.

   o Torsion general is broken? Yes (argh!)
     Am I using the right version of mgtree?
     ::: 8

* Done - yay!

   o Fix the documentation generation - coot.html ::: 2 

* Done - now part of the source bulid.

   o OXT atoms are added after TER atoms? ::: 1

* Done.

   o Fix ligand chi angles.  

     Try rotating round CA-CB in a modified CYS (after clicking on a
     CA). [Ian Tickle]

     ::: 4

* Done - works fine.

   o Read a map, Sharpen map -> crash ::: 1

* Fixed.

   o Can you fix the geometry analysis plot so that the correct
     largest geometric outlier is shown? (puntable) ::: 1 

* Looks OK, after some consideration.

   o Try different rotamers on Add Alt Conf. Ashley Pike and others
     ::: 1

* Done.

   o Addition representations: "All off" button needed.  ::: 1

   o Water removing problem from Takaaki Fukami ::: 1

* Can't reproduce.  Added index protection.

   o ^G I1  -> spins instead ::: 0.5

* Done.

   o Put "Set Matrix" under the R/RC button dialog. ::: 0.5

* Done

   o Can you fix the bonding of the oxygens in tlc 2AB? ::: 1

* Yes.  Not too hard.

   o Difference map peak in large continuous ligand needs filtering,
     if possible (making clusters?) - puntable ::: 2

* Done - It is much better now. It does seem to fail a bit, but not
  much (2 peaks in the ligands site).

   o Average maps function (take a list of maps). ::: 1

* Done.  In scripting anyway.


   o Add clash score to backrub rotamer - consider making dist_crit
     smaller. Test with residue A19 in low res map ::: 2

* Done.

   o "make check" should be clean. ::: 1

* Done.
 
   o Get News seems to be failing for me -> nothing. ::: 1

* Done.

   o Insert reference into docs: "The Backrub Motion: How Protein Backbone Shrugs
     When a Sidechain Dances" Structure, Volume 14, Issue 2, Pages
     265-274 I. Davis, W. Arendall III, D. Richardson, J. Richardson
     ::: 0.2

* Done.

   o COOT_SYS_BUILD_TYPE is wrong on Ubuntu 64 ::: 1

* Done.

   o Need to fix up assign sequence and add-terminal-residue so that
     the sequence offset is taken into account properly. ::: 2 
 
* Done.  Using running sequence number.

   o Multi-refinement falls over at the end sometimes - missing
     residue? ::: 1

* Done.


   o Align and mutate is crashing: 

#6  0x00000000006cf4a4 in molecule_class_info_t::align_and_mutate (this=0x1a3, chain_id=
        {static npos = 18446744073709551615, _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, _M_p = 0x1a989f0 "P%G�%@>\222|\177"}}, fasta_seq=<value optimized out>)
    at ../../coot/src/molecule-class-info-mutate.cc:425
#7  0x00000000005d5a7e in graphics_info_t::mutate_chain (this=<value optimized out>, imol=<value optimized out>, 
    chain_id=@0x7fffa0e7b110, seq=@0x7fffa0e7b0f0) at ../../coot/src/graphics-info-mutate.cc:302
#8  0x0000000000503726 in do_align_mutate_sequence (w=0xe56430) at ../../coot/src/c-interface-gui.cc:5073
#9  0x000000000055250d in on_align_and_mutate_ok_button_clicked (button=<value optimized out>, user_data=<value optimized out>)
    at ../../coot/src/callbacks.c:7977
#10 0x00007f7c8e0ab27d in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#11 0x00007f7c8e0c0e3b in ?? () from /usr/lib/libgobject-2.0.so.0

    ::: 0.5 

* Fixed.

   o Pukka-puckers? should now use the N1/9-C1* bond not the base plane. 
     What is the critical distance, now that we are not using
     out-of-plane distance? 3.0 says Jeff.
     ::: 2


   o With align and mutate so that the sequence offset is taken into
     account properly.  Check that the subsequent refinement of
     residues only refines the insertions and mutations, not the whole
     structure - consider using interruptible-fit-protein or something
     like that were the specs are passed (interruptible-fit-protein
     may need to be refactored). ::: 4

* Done.  Harder that I thought.
 

   o In Align vs PIR, the resulting dialogs tries to go to the CA atom
     of the residue to delete, this doesn't work for phosphates,
     waters etc.  Do better at getting a sensible atom name to go to.
     ::: 1

* Done.

   o audit strncpy()s. ::: 1

   o audit GtkPositionType usage for use with strings.

src/c-interface-build-gui.cc      done
src/c-interface.cc:               done moved to -gui.cc
src/c-interface-gui.cc            done
src/c-interface-superpose.cc:     done
src/c-interface-validate.cc:	  done
src/cmtz-interface.cc:            done - hideous code.
src/graphics-info.cc:             done
src/graphics-info-modelling.cc:   done
src/graphics-info-refmac.cc:      done
src/graphics-info-superpose.cc:   done
src/gtk-manual.cc:                done

   o Autofit rotamers for Leucines is doing the right thing?  Test on
     2dk2-overlayed-fix-up-mutated-close.pdb.  It seems not.  Other
     residue types suspicious ::: 2

* Done


   o Random-looking crash on multi-refine with Ramachandran
     optimisation. ::: 1

* Can't reproduce.

 
   o On update the rotamer plot with waters in the chain (e.g. 2qlu)
     lots of text complaints in the terminal about quads for waters. :: 0.5

* Done


   o On refining (Key T) the green spot disappears from the Rama plot.
     Also disappears on click click refinement. ::: 1

* Done.

   o Does PISA (interface) work on various computers? ::: 2

* Needs bug fix.  OK, now need moving to Extensions.

   o sulfur-sulfur bonding  ::: 0.5

* Done. 

   o In the Display Manager "Show Additional Representations" needs to
     be hidden when the addition representation vbox is hidden (and
     shown when the vbox is shown)  ::: 0.5

* Done.

   o binary in output on many delete waters. ::: 1

* Done.

   o transformed maps take on the cell+symmetry of the reference
     coordinates.  If reference coords do not have cell and symmetry,
     stop.  Needs symmetry operators to symbol interconversions.
     ::: 2

* Done.

   o transformed maps take on the symmetry of the reference coordinates 
     ::: 1

   o Crash on Mac on closing 
     (set-go-to-atom-molecule 4) after the (post-go-to-atom-window)
     should change the Go To atom dialog.
     ::: 2

* Done. Yay!

   o Fix problem of Go To Atom dialog displaying the wrong molecule
     number on post-go-to-atom-window (see dnotes).  ::: 1

* Done. I hope.
 
   o Occupances on alt confed residues are wrong.  Make a test ::: 2

* Done.

   o Add jiggle-fit for ligands ::: 3

* Done.

   o delete_atom() needs investigating.  Spews binary? ::: 1

* Fixed.  Was dereferencing out out date char * pointers.

   o If you set a view name it gets ignored in the current views panel
     (but the name is OK if the views panel is closed and re-opened) 
     ::: 1

* Done. One liner (typo, probably).


   o Stereo (hardware, side by side) Add-reps.  Need to update the
     display list objects when the GL context changes. Need to store a
     GL display list number for the alternate GL context in side by
     side mode? 

     When switching stereo contexts creating a new GL context, we need
     to run update_additional_representations() for each model molecule.
     ::: 3

* I won't waste time fixing this exactly.  I am happy that we get 2
  representations of ball-and-stick objects in side-by-side stereo now.

   o dictionary for LEU, chi angles wrong, chiral centre for CG should
     be negative, not both. Check other residues,
     THR VAL LEU ASP ASN GLU GLN ILE ::: 2

* Done.

   o Pierre Aller rotamer bug.  who knows how long this will take?
     Horrific. ::: 1

* Gone away.


   o Put the GNU GPLv3 in the GUI ::: 0.5
 
* Done.

  o add-view-description fails.  Needs fixing. ::: 0.3

* Done.

  o assign-pir-sequence: does it say to which molecule it has been
    assigned?

* Done

    assign_sequence() needs to be in the history 

* Done.
   
    ::: 0.3


  o Use positive/negative/both or whatever (what is -2?) in edit restraints
    chirality [Andrew Leslie]

   ::: 0.5

  o where are the links in 1e3z.pdb?  do we get links from 1OHY.pdb?
    mmdb version problem perhaps.

    Fine, it seems like an mmdb bug.  ::: 0.2

  o Distances in the SSM align output are wrong.  e.g. Frank's test.
    ::: 2

* Done.

  o Add the alignment for post-ssm superposition - put it in a gui
    too?  ::: 3

* Done.  Not a GUI atm.

  o Environment distances: examine the residue type, look it up in the
    dictionary: only if this residue and that residue are not a
    polymer should you not draw the lines (don't rely on the residue
    numbering).  JED ::: 1

* Done.

  o Test CNS data sharpening ::: 1

* Done.

  o Gap penalty too low in alignment?  OK, I can't seem to change the
    results, no matter what gap penalty and extension penalty I
    use.  ::: 2

* Done, it seems to me.  Bob's example now looks good.

  o Try: All Molecule -> Stepped refine on a CA-only molecule.  That
    seems OK, how about "Fit Protein"? OK, it's Fit Protein that is
    the problem ::: 0.5

* Done.  Check that there are more than 3 atoms in the residue before
  trying to rotamer and refine it.

  o Replace with new dictionary. ::: 0.2

* Done.

  o Kevin Keating map peak position problem :: 2

* Done? Needs testing.

  o nudge monomer/residue (Ctrl-arrow keys) to move residue at centre
    up/down left/right. Has to be done internally, I think, but
    compare with function in nudge-screen-centre-gui.  Puntable, but
    cool. ::: 1

* Done.  It is cool.

  o density-fit graph should update on deleting a residue (and water) ::: 1

* Done

  o Backrub rotamers compensatory peptide rotation ::: 2

* Done.


  o Deleting molecules and running refmac somehow causes a crash? ::: 2

    1: deleting the go-to-atom molecule in the close molecule dialog
       does not delete/update the residue and atom tree.  It should.

       Fixed

    2: deleting the go-to-atom molecule in the Display Manager does
       not change the internal go-to-atom molecule, even though the Go To
       Atom dialog moves on to the next molecule.

       Is this true?  No.  

       But, the option menu of the GoToAtom dialog does not change on
       deleting the Go To Atom molecule using the Display Manager.

     ::: 2

* Done.   

  o Fix refmac interface crash (needs python, I guess) on Bill's
    stand-alone Coot 0.6-pre build:
    In run refmac: Choose MTZ file for Refmac -> dialog -> open -> crash.
    ::: 2

* Bernhard has fixed this already?  Probably not, he says.  Can't
  reproduce.  Shelving for now.

  o In editing the comp-id (or 3letter code) in the restraints editor,
    we should generate a new dictionary entry, not the same as we
    started with. ::: 1

* Done.

  o GTT dict from Adrian?  I am confused.  The current dictionary for
    GTT has the same chiral centre sign as LYS has at CA1.  Keep the 
    original one for now. ::: 0.2

* Considered.  Nothing changed currently.


  o A function that associates the current chain with the lastest pir
    file. ::: 0.5  

* Done.  Sent.

  o Fix NAN crash in Refinement of AUC in gold-lysozyme. Rick comment.
    Data on stick (Icanmakecootcrash). Not reproducable on ubuntu
    laptop. Not reproducable on 64 bit ubuntu either. Needs Bill's
    standalone Mac binary ::: 4

* Not fixing this now.

  o Add in Dale's BCL dictionary.  ::: 0.2

* Done.

-----
