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dnotes-2008
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Things to do for 0.5.1
1 Things, 1hd.
o 1h4p NAG: it doesn't refine - even when I read in the dictionary
by hand. What's going wrong?
o Pucker of ideal DNA need to be fixed. Needs better reference nucleotide.
1hd.
* Done. Not tested :-/
o Nucleotide builder - with B form RNA need to be fixed. Needs O2'. 1hd
* Done.
o [Maria Håkansson] Hydrogen fail to move in SHELXL molecule when using:
add alternative conformation
edit chi angles
Confirmed fail - uses dictionary?
real space refine
Of course
rotate translate zone
Works for me.
* There is no quick solution for this - SHELXL has systematically
different hydrogen names. Needs an email to Maria. Done.
o Do the fat bond and Ball & Stick rep get updated on moving
residue/sidechain?
* Fixed.
o Draw -> Additional Representation -> This residue -> Ball & Stick
Gets drawn in fat bonds too. Bad.
* Fixed.
o Reset View needs fixing.
* Fixed.
o "the molecule chooser dropdown in go to atom is not updated on
copy fragment." - JED
* Fixed
o Loop building in both directions for scheme. Needs checking from GUI.
1hd
* Done.
o Ramachandran fixup in Extensions - does it need more residues to be refined?
* Done.
o clean up this debugging:
DEBUG:: GetSelIndex (make_flanking_atoms_rama_restraints) returned 3 residues (for flanking rama restraints)
DEBUG:: --------- :: Adding RAMA phi_psi_restraints_type
Adding RAMACHANDRAN_RESTRAINT
* Done.
o Open Distance and Angles dialog, open a new one, close the new
one, take a distance on the old one -> crash. We need to not open
a new one if there is an old one and we need to raise and
unminimize the old one.
* Fixed.
o (set-view-quaternion 0 0 0 0) in 0-coot.state.scm file [written
when using --no-graphics preivously (perhaps)].
* Fixed.
o Test that manual-ncs-ghosts averages all the maps for NCS > 2.
Jianghai Zhu <[email protected]> 3 Nov 2008. (I mean, add a test,
that'll be fun).
1hd. Do this in the office.
* Done. Not added to test suite though. Looks... OK, but not ideal results.
o restraints editor:
edit ASN
save
edit CYS
save
Look at monomer-CYS.cif, the TLC is ASN.
0 or 2hd.
* Looks fine on FC4, still bad on MacBook? Pass on MacBook - too difficult.
o LSQ map by overlap - does that work properly? Use an offset
reference molecule. You can test this by summing the density
before hand, rotation/translating the map and then re-summing the
density on the transformed map.
2hd.
* Seems fine.
o remove debugging:
Gtk2 text view code...
* Done.
o make_dynamically_transformed_maps() needs an extra arg to tell
whether or not to overwrite maps that already exist with that given
name (instead of creating new maps).
* Done.
o in the Restraints Editor monomer selector, the last residue should
be the active item.
* Done.
o Does molprobity (specifically reduce) work with modern distros and
do the right thing in Coot. Check (set-do-probe-dots-post-refine 1).
* Works.
o Add "Make 4mer-XYS" to the advanced tutorial.
* Noted.
o Look at build-coot-fc4-gtk2/src/Ideal-B-form-DNA-interesting.pdb.
Make a fixed atom on the O3* of 1A. The refinement fails now (no
progress). Is that because of make_link_restraints() is not taking
into account the fixed atoms? Could well be, because if I delete
residue 2 in that chain, then the regularization (with that atom
fixed) works fine!
1hd
* Looks good now. Well, the fixed atom moves, but the minimization
completes succesfully now.
o Mail B re: changes to manual-ncs-ghosts.
* Done.
o Make a function that colours by a function that returns a value
given an atom spec.
o on build-latest-coot on bubbles:
! LaTeX Error: File `graphicx.sty' not found.
1hr
* Fiddled. Needs examining of the logs. Still is failing. Fixed now
I think. TEXINPUTS.
o Add a function of molecule-class that returns the position
(if posible) of an atom given a string e.g.
"A" -> nearest atom in the A chain
"43" residue 43 of the chain we are looking at.
"21b" -> residue 21 of the "b" chain, otherwise residue 21 of the "B"
chain
* Done.
o update map without generating a new molecule.
Perhaps the NCS maps, or read a new map from MTZ updating a
already existing map.
* Done.
o Add a function of molecule-class that returns the position
(if posible) of an atom given a string e.g.
"A" -> nearest atom in the A chain
"43" residue 43 of the chain we are looking at.
"21b" -> residue 21 of the "b" chain, otherwise residue 21 of the "B"
chain
* Done.
o info-dialog history string needs quotes
* Done.
o remove this debugging (on making NCS ghosts):
INFO:: max_xmaps :0
INFO:: xmap_list :0
* Done.
o Makefile.am in share/coot/python - bad.
* Done.
o in make_link_restraints() use
class bonded_pair_t {
CResidue *res_1;
CResidue *res_2;
std::string link_type;
};
Write:
bonded_pair_t::try_add(CResidue *r1, CResidue *r2, std::string link_type)
which only addes a bonded_pair_t to the vector if this link is not
aleady in the vector. Hmm.. container class?
std::vector<bonded_pair_t> bonded_residue_pairs = bonded_residues(int SelResHnd);
i.e. make a function that returns this then simply run through the list.
* Done, with avengance.
o on building an non-python version:
/home/emsley/autobuild/Linux-koala-pre-release-gtk2/lib/python2.6 does not exist
also on bragg3:
/y/people/emsley/autobuild/Linux-bragg3-pre-release-gtk2-python/etc does not exist
/y/people/emsley/autobuild/Linux-bragg3-pre-release-gtk2-python/html does not exist
/y/people/emsley/autobuild/Linux-bragg3-pre-release-gtk2-python/bin/pythonpython2.6 does not exist
/y/people/emsley/autobuild/Linux-bragg3-pre-release-gtk2-python/bin/pythonpython2.6-config does not exist
/y/people/emsley/autobuild/Linux-bragg3-pre-release-gtk2-python/include/pythonpython2.6 does not exist
* Fixed.
1hr
o update map without generating a new molecule.
Perhaps the NCS maps, or read a new map from MTZ updating a
already existing map.
Punt to 0.6.
o Schubert, Carsten [PRDUS] bug:
Test that the following work with and without command line args:
coot --pdb my.pdb --auto my_map_coeffs.mtz
set_model_fit_refine_dialog_position()
set_delete_dialog_position()
set_rotate_translate_dialog_position()
* Seem fine to me witout args. And with args. i.e. it works for me,
can't reproduce.
I tried both the python and scheme commands with the same lack of effect.
o The chiral restraints for GLS (a spiro compound) are not appearing
- they do for ASP though. Hmm...
This is because they get rejected at the stage where the volume
sign is check, currently it needs to be NEG or POS. If it is
BOTH, we need to be careful that it can be available to be
reassigned and that when it is BOTH, no retraint is added (or we
could be more clever and work out which restraint should be used
(is closest) by looking at the geometry of the atoms involved).
1hd
* Fixed.
o save_restraint_chooserdialog in glade, the response is not
working or not closing the dialog. Maybe its a Mac thing. I
can't see how this "close/cancel" button is supposed to work.
I can now. Use GTK_RESPONSE_CANCEL.
Remove this debugging though:
restraints editor saving 0x90065b8
debug:: testing restraints editor number 0 of 1 0x90065b8
debug:: testing restraints editor number 0 of 1
comparing 0x90065b8 vs 0x90065b8
restraints editor index 0 matches
Returing restraints editor with dialog 0x90065b8 from get_restraints_editor() from dialog 0x90065b8
* Done.
o Fix up clipper (21ac)
* Need to use new clipper. Done.
o Build a helix in 1b41 map. The Spacegroup is R 3 2 but the cell
is hexagonal.
2hd
* OK, need new clipper. Applied.
o Make l toggle label for this closest atom.
* Done. It adds a label, not toggles.
o Fix rotamers for residues with ins codes e.g. gui rotamers on 52A H
chain of 3hfl. And autofit rotamer.
molecule-class-info-other.cc:1414, is the moving atoms asc for
residue 52 or 52A?
* Fixed. Test added.
o Pick on an active atom should flash the atom.
* Done.
o Can you enable the 'X' key for residues with alt confs?
* Yes, done.
o Coot fails to read 293.cif. I want to be able to parse it
correctly and get the coordinates from it.
2hd.
* Done.
o Can you enable the 'X' key for residues with alt confs?
* Yes.
o remove debugging ======== new version
* It's gone.
o Build a helix in 1b41 map. The Spacegroup is R 3 2 but the cell
is hexagonal.
2hd
* OK, need new clipper.
o goosh is part of guile main now?
* Nope.
o Baton-build, cancel, baton build again. There is no Baton Atoms
molecule. Why?
* Can't reproduce.
o Bernhard we need a COOT_PYTHON_EXTRAS_DIR, a directly of *.py
files that Coot reads/evalutes on start up. (If, of course
COOT_PYTHON_EXTRAS_DIR is define and is a directory).
* Bernhard has done.
o DEBUG:: rotamer_probability_tables self test passed
* cleaned
o Look at rotamer graph, make a modification, look at rotamer graph
again. The blocks have been scaled down [JED report]
1hd
* Fixed.
o Flip peptide needs to flip the H on the N too. [Joel Bard].
* Done.
o Edit the Coot page on the CCP4 wiki: put a link into Kay's page.
* Done.
o I have taken the setting of transient out of
store_geometry_dialog(). Now on_distances_and_angles1_activate()
needs to set it's dialog as transient explicitly.
* Done.
o Geometry graphs (rotamers at least) are transient and annoying.
* Nope. It's a window manager issue.
o Enable the torsion of a ligand when in CA+lig display mode [Ingo
Korndoefer]
* Done.
o Fix Frank's problem of Keybindings when using F8 bin with python
and scheme keybindings.
* seems OK to me now.
o Don't tar up python files for a non-pythonic build.
* Done - sort of. I have not got rid of the python libs.
* Fix by making python builds build in their own directory.
Needs changes to build-it - non-trivial.
build-web-page-builder.scm needs to change to follow the
new places for the python build info.
o Do the P backbone.
* Done.
o Crash: Using the display manager delete molecule buttons (CentOS
build)
* Fixed.
o Need to make cootrc gtk1/gtk2 specific - see fixes/cootrc on the
web site
* Done
o are test-wiggly ligands written to disk by default?
* No.
o test that fixed atoms with alt confs work.
* Looks good to me.
o Read a shelx file with PART 1 10.6 [Mirek Gilski] [10.6 is the
site occupancy factor]
* Done.
o put the NCS edit test into greg-tests.
* Done
o Rework the Extensions dialog to make it less long.
* Done.
o Add a Delete button in display manager
* Done.
o green torsion bond hilighting has disappeared.
* Done.
o do_rotamers() given imol, chainid, resno, inscode, altconf.
Attach it to active atom and a key binding. FvD
* Done.
---
Things to do for 0.6
o Rotate translate chain/molecule
o Edit a SHELXL file before refinement
o backrub on rotamer search
o PISA output display
o multi-residue range for RSR - eg in residues in a sphere
o redo sequence view
o Helix fitting overshoots
o Do ligand fitting from a given place (don't blob search).
o P backbone mode
* Done in 0.5.1
--------
Things to fix before 0.5
127 Done.
o 'Refinement Options GUI' for scheme
Done.
o Crash: from JD.
Another crash from JD: on closing molecules.
* These are the same thing, the use of (or destroying of) a radio
button group for the maps in the display manager. I tried to debug
with valgrind, but could not reproduce.
o crash:
./coot-real pdb coot-download/pdb1rt9.ent --data 1e2k_sigmaa.mtz
create/read in map
reset view
-> crash
(note, I had typed pdb not --pdb
pdb1rt9.ent is not there at time of writing)
* Fixed, stupid trivial mistake.
o --flood crashes. Something to do with clipper symmetry.
* No, not really, it was to do with the mtz filename being wrong and
trying to mask the map that was not filled.
o Bill Scott's python problem: 2hd
I can get rid of the problem by hacking "ivector FF1,FF2;" out of line
211 in ssm_superpose.h
First, get Coot to compile on a Mac... (sigh)
Well, Bill has sorted this out now... not so much a priority.
o Tell Bernie: Need a gui preferences for torsions that move
hydrogens (in response to Klaus Piontek 30 Aug 2008)
* Bernie says do it the proper way, make (or make sure that) the
hydrogens rotate even though we are rotating chi1 (say). He is
right.
* Done.
o update README. coot clipper and mmdb info up to date?
Done.
o TS: Check that the ramachandran button/accept reject info works
(is set to a sensible name).
Bleugh. Have to build a gtk1 version..
* Built and fixed.
o I fiddled with generic-single-entry. Make sure that it works.
* Seems to.
o Bernie: Delete, Keep Active, delete zone click click then delete
zone again click delete the wrong atoms.
* Fixed. This is an example something not caught by automated tests.
o Delete atom (or waters perhaps) with "keep delete active?"
active turns the cursor to normal "move", not the pick cursor,
which is confusing.
* delete, water, atom and residue all behave.
o Atom selection error? pdb2qc1.ent additional representation B 97
101 "" ball and stick -> just one residue selected (or did I make
a typo?)
Atom selection by string works OK.
* A typo, I guess. It seems to OK now.
o Test Steven's 3CH6 for NCS chain skipping problems.
* Is fine, except the usual sliding problems when too close to the
paired residue.
o check that 1xu1 works with NCS jumping
* Is fine.
o write an internal test for the atom selection (in selection and
inverted) (test the number of atoms in each will do, I guess)
o check the console when rotating the hh1 (hydrogen torsion) of a
TYR.
118 Done.
o Robert von Dreele: test that nZ is divisible by 3 for hexagonal
axes. See mail from Kevin.
* It's a clipper issue.
o Finish A-RAPPER-gui, penelope. 2hd
* see what Nick says. He says it shouldn't crash. No progress. Punt.
o PDB v3.0 compatibility. 1hd
* Done. As of mmdb-1.12
o fix writing restraints from restraints editor.
* Done. If tlc is not set on rendering the restraint, then copy the
comp_id to the tlc.
o Use Eugene's new LINK-reading code < 1hd as above
* It reads LINKs, now what?
o chi squareds are displayed properly on GTK1 version? kalypso - 1hd
o Correct CISPEP if needed cards on writing pdb. <1hd - depending
on new mmdb code.
o need fixup for gtk_combo_box_get_active_text(null). jackal 1hd
* Done.
o -c script is half done. impala. 1hd
* Done.
o build-hardy-python makes a build where cootaneer_bl_gui fails (on
some python lib). pygtk failed to be configured? 1hd
o N terminal residue addition (with valgrinding?)
* Done.
o Why does the residue type not work when adding a new residue?
Because (set-add-terminal-residue-default-residue-type "UNK")
perhaps?
* Yes
o documentation for NCS chain edits
* Done.
o the scrollable map needs to be (correctly?) saved in state file. 1hd.
* Done.
o Kevin's Ramachandran Refinement target, 8hd
* Done
o Problem with (run-python-command "cootaneer_gui_bl()"))) when
pyobject and pygtk don't get built? Roni Gordon.
* Fixed.
o put the manual in Oxford.
* Done
o Jan D. crash.
* Nvidia driver problems is my guess
o Side by stereo with (and without) display-lists for maps
* Done.
o HK's 3 map crash?
* a sentinel issue, I guess, Fixed, but keep an eye on it.
o "key bindings" in the manual needs to be updated.
* Done
o Ca Zone -> Mainchain on a short range should give back useful
feedback. Confirmed - needs some feedback. An info dialog (fragment
too short - needs to be at least 6 residues).
* Done.
o rotate/translate fragment about fragment centre fails when
clicking on sliders. However, by mouse control, it works.
* Done.
o plane restraints being set in gui, dismiss dialog, open dialog ->
plane restraints seem unset.
* Fixed.
o plane restraints should be saved in state file, if it is not the
default, i.e. if they are off.
* Done.
o set-matrix state not saved in state file.
* Done.
o refmac-extra-params as a function need documenting.
* Done.
o Need to check torsion restraints
and wiggly ligands
get_torsion_bonds_atom_pairs() in wiggly ligands?
and Edit Chi
now that I have enabled the reading of CONST torsions.
How about a test for wiggly ligands and then we can put this
item to bed. 2hd
* That will do for now. BUA looks good, and I suspect 3GP looks bad
(broken bonds) because the dictionary is wrong.
o (assoc-ref (monomer-restraints "TYR") "_chem_comp_chir") extra
list layer? [JED]
o Fix the comp_id on exporting monomer restraints to a file. 1hd
* Done
o rev 1217 is good, rev 1218 causes glade-2 to crash on coot-gtk2.glade
* Fixed, for now.
o Reference for EDS:
Title: The Uppsala Electron-Density Server
Author(s): Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wahlby A, Jones TA
Source: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60: 2240-2249
Part 12 Sp. Iss. 1, DEC 2004
o Make names for map transformation better - both the new
coordinates and the new map (use set-molecule-name).
* Done.
o Check Richardson Rotatmer library is correctly used for GLN, ASN, PRO.
Ask about Rotamer misses. Well, the dictionary is fine. Why does
molprobity web site gives less bad rotamers then? (First: Does it?).
Yes it does: e.g. for 1sar molprobity notes only these:
"Bad rotamer B 47 GLN (0.3%)" agreed
"Bad rotamer A 91 LEU (0.4%)" agreed
"Bad rotamer A 13 PRO (0.9%)" hmmm - it agrees.
"Bad rotamer B 41 GLU (0.7%)" don't see why it is bad, but it agrees.
There are 10 times more for Coot.
(fix-nomenclature-errors doesn't fix anything). 4hd.
* Done. More like 8hd, actually, when alt confs were added.
o refmac-runs-with-no-labels, c-interface-info.cc (wrong place for
this?) <1hd.
* Done.
o Question: does guile-lib work for guile version 1.6.x ?
* Yes, it does.
o Can the map transformation interface be clearer? Can I GUI
interface the most frequent usage? 1hd
* Done. It was done already - I'd forgotten.
o on opening the about dialog:
** (lt-coot-real:18431): WARNING **: Couldn't find pixmap file:
coot-icon.png on kalypso
* Done by Bernhard
o Make a test pdb that exercises Case 3: model has deletion in
align_on_chain(). (tutorial-modern.pdb exercises it, but the
deletion is at the end of the A chain). Make tests where the
deletion is at the N term and in the middle of the A chain. 4hd.
* Done.
o crash on delete residue range: Harri Jayaram
The steps I did were
1) Start fresh coot
2) Get coords from pdb - get-ebi-pdb 1OTS
3) Centre on chain A residue 39
4) Bring up delete residue GUI
5) delete from residue 17 ( n terminus) to residue 37 or 39 (I
forgot which one)
6) Coot beachballs and takes machine down with it
Very slow. Some fumbling of atom picking needed to tickle this?
1hd.
* Can't reproduce now.
o side by side stereo with dislay lists. 4hd
* Gone away, or I've fixed it or I've forgotten what the problem was.
o Ethan Merrit's bugs on window sizing.
Partially fixed. gtk_widget_set_usize() in
set_graphics_window_size() now replaced with gtk_window_resize()
on a GtkWindow() (not the glarea).
g.graphics_x_size is used inconsistently. It is a bad name. It
is (now) used for the window size (c-interface-gui) and the
glarea size (glextras()). Both need to be stored gl_area_x_size,
gl_area_y_size, main_window_x_size, main_window_y_size.
This is no longer true.
o Change into side by side stereo mode. Resize the window. Now
views are of different size/aspect ratios.
* Fixed.
o Test/fix hardware stereo in Gtk2 mode. See also Randy Read's
message about going to wall-eyed and the state of walled eyed in
the status file.
Note also Joel Bard's comment about the problem of non-updating
density lines after switching to (or attempting to switch to)
hardware stereo mode.
2hd
* Done. Well, very nearly. When coming out of side by side stereo,
still the map disappears. Other than that it all seems OK.
o check the number of saves on Eigen flips. On undoing, it seems I
have to undo twice for each step.
* Done.
o Make ball and stick mode to work in Additional Representations -
I want to be able to turn them on on off with a check box. 2hd
* Done.
o fix build-it-gtk2-simple so that it does not run the tests when
run not in York etc.
* Done.
o Add an Alt Conf to a MSE. Fails to display all atoms. Edit a
file and read it in. Now refine. Longer bonds? 3hd
* Done.
o look at the fail-recentre .scm state file (penelope gtk2). It
fails to try to centre on a molecule other than 0 it seems (from
the status bar). <1hd
* Ignore this. Molecule 0 was the same as molecule 4 (molecule 1 was
different). When finding which molecule we were centred on, Coot
chose 4, even though it had been on 4 and centred on 0 for the next round.
Pathological case.
o check that newly read cif file overwrites the restraints of the
previous restraint set (e.g. delete a restraint and see what
happens) < 1hd
* Done from scheme level. Need testing from GUI.
Done.
o make the reset view work only for coordinates molecules. <1hd.
* Done.
o Re-instate (and bug fix) the molecule-number greg-test in
08-utils.scm. 1hd
* Done.
o Do not display hydrogens in intermediate atoms in refinement if
they are not displayed in the "static" atoms.
* Done.
o Does Replace Fragment work? Can you write a test?
* Yes, it does. Yes, I can.
o In Key bindings GUI, show the key bindings from python also.
* Done.
o Document eigen-flip in user manual.
* Done.
o Draw zero occ spots in colour by chain mode [PRE] <1hd
* Done.
o Add Terminal residue with on to a residue with a TER. (TER must
disappear) 2hd.
* Done.
o Add means to get to fix/anchor atoms in gtk1 version.
* Done.
o NCS loop (or whatever it's called (Copy NCS fragment?): when
there is a difference of residue name, then the old name should be
replace by the new one. 1hd
* Done.
o Open Bond Parameters dialog with no molecules loaded -> crash
* Done.
o Addition of waters using GUI in a shelx molecule puts waters in
with occupancy 1.0 [Tobias Beck]
* Done.
o NCS jumping with a 2 x heterotetramer (or some such) 2hd
* Done.
o Add Terminal residue with on to a residue with a TER. (TER must
disappear) 2hd.
* Done.
o Addition of waters using GUI in a shelx molecule puts waters in
with occupancy 1.0 [Tobias Beck]
* Done.
o SFAC needs to be written higher in the shelx ins file, after UNIT
line.
* Done. Before, in fact.
o check that newly read cif file overwrites the restraints of the
previous restraint set (e.g. delete a restraint and see what
happens)
How shall I test this? use monomer-restraints, delete a bond
restraint between a given atom pair (e.g. cb cg in a tyr), copy
a TYR from imol-rnase, refine. As there is no bond restraint,
cb and cg should fly appart to 3A or so.
* Done.
o Do a refinement on 3bv2 in CA + ligand mode. It changes the
colour scheme to rainbow representation.
* Fixed.
o multi-carbo.pdb contains 2 residues that should have a glycosidic
linkage. However, the regularization on it fails (they move
apart). Why?
Because, d'uh, I'd tried to connect the monomers the wrong way
round.
Make a test. Test on the distance between atoms in
the link.
BETA1-4 1 O4 2 C1 single 1.439 0.020
need function (return a boolean):
(bond-length-within-tolerance? atom-1 atom-2 ideal-length tolerance)
o It would be better (faster) if the carbo test was fitting into
density, rather than regularizing.
* No, it wouldn't as it turns out.
o Glycosidic linkage needs to be 3A not 2A.
* Done.
o get an alanine - with hydrogens. Refine. undo, refine. check
hydrogen positions.
* Fixed.
o Pierre Aller:
I am using the last version of coot with an imac Os 10.5.2 intel
core Duo. I download coot via fink, and since one or two month
coot freezes a lot. It happens always when I am using "Measures"
and "residue info".
* Crappy X11, I'd say.
o The default occupancy for new atoms in a shelx molecule should be
11.0. Is it? [JED]
* It is, but the residue number is "1" and the SFAC index is -1. Bad.
Fixed now. Note SFAC line is now moved in the output .ins file.
o Fix up Addition Representations in Display Control. Don't
display if empty.
* Done
o Reading in a shelx molecule should reset reset the view.
* Done
o on adding a a Mg atom by widget:
(lt-coot-real:4004): Gtk-CRITICAL **: gtk_widget_destroy: assertion
`GTK_IS_WIDGET (widget)' failed