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TODO
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-*-text-*-
What's Planned for the Upcoming Coot Releases?
-----
o Refine a cyclic peptide ligand. Make links and modifications as needs. Feel the pain.
o 2xkm is problematic when reading/converting the data.
o Do we use JLigand.scm in jligand interface script?
-----
Release 0.6 and 0.7 [Sept 2009, Dec 2011]
Top commitments:
o Edit a SHELXL file before refinement
* Done.
o backrub on rotamer search
* Done.
o Helix fitting overshoots
o PISA output display
* Done
o In the restraints editor, the volume sign should be displayed as
a string (generated from volume_string_int)
* Done
o Make ligand fitting work from a given position (find the blob
centre close and do the orientation search there)
* Done.
o P backbone mode
* Done.
Like to do:
o redo sequence view
* Done.
o Fix 64-bit coot problem(s)
* Done.
o Add "centre molecule here" check button for reading coordinates
Kevin M.
* 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.
* Done.
o enable --splash-screen
* Done.
o "CA mode" for nucleic acids should draw a P and C1' trace. [VR]
Priority: 10, Difficulty: 4
* Done.
o Does the window stay constant size (on something other than a
laptop) on start, exit, start exit cycling?
Priority: 6: Difficulty: 4
o The lib dir should be set with AC_CHECK_LIB, not just "lib". Tim Fenn.
* Let's hear from Tim Fenn. OK, he replied. Non-trivial. OK, Punt to 0.6
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 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. Punt.
* Done.
o Check out the virtualbox page on the ubuntu wiki for info about how
to set it up. Punt.
o What's crashing on using NCS in Bill's 0.5 build? No idea.
* Problem gone now, I think.
o 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).
* Done.
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.
* Done.
o Rotamer plots need to update on multiple do/undos.
o Now that we have sequence aligmment, how about supporting the
mutation (to the assocated sequence residue type) of the residue
that I'm looking at [James Whittle] - needs a function
(associated-sequence-residue-type imol chain-id resno ins-code)
-> 3-letter code or #f
o in coot_toolbuttons.py Bernhard registers the icons. Does that
make them smooth?
* Not relevant now.
o Phil Evans wants colour by chain as the default. Can you make
this the default at coordinates read time (similarly, others want
CA mode).
o Put globularize protein into Coot. Make it a bit more clever?
o Garib wants a function to move waters close to the protein.
* Done.
o Do the tutorial. Are the blob numbers correct? (EJD 1008 May 23
suggests not).
* Seems fine
o check the "movie" interface
* Is OK now.
o Use LSQ for NCS matrices - need to be user setable option.
* Done.
o Add the reading of a good map and a CNS map to tests.
* Done.
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? Man, this will be powerful, if I can make it work. Don't
forget to also rotate the mainchain hydrogens. Does
is_mainchain_atom() working for mainchain hydrogens?
* Done.
o Investigate interupting long fitting/Post MR tools [JED request]
* Done.
o add a mechanism where we can register functions to run after
refinement and/or regularization.
* Done.
or deleting things says JED. In fact, a funtion to run that is
attached to a molecule (somehow) on any update/change/manipulation.
* Done.
o Fix the DNA/RNA names test (penelope gtk2 old-tests). 1hd
* see what cootbb says... Bill says add it (currently is skipped).
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...
* Done.
o Fix up mini-RSR so that it compiles properly.
o Use libglade
* Done.
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.
o Move widget functions in c-interface-build.cc to
c-interface-gui.cc (or consider new c-interface-build-gui.cc).
o Dynamic distances define need a pick cursor.
o Put refine-zone and regularize-zone into the history.
o multiple residue ranges, glycosylation, covalent bond entities
* Done.
o Redo sequence view
* Done.
o check that the puckers of the ideal RNA/DNA is correct for A form
and B form. Try to find matrix example nucs for Z form.
* Done.
o Centos/RHEL 4.6, has gtk2 version 2.4.13, fails to compile
guile-gtk-2.1 out of the box. It didn't know about GtkAboutDialog,
I think. Also there were some extranaeous ^:^s in the .x
files. 4hd.
Not going to get the hardware in before 0.5 is released. Punt for 0.6.
* Done.
o Hydrogens from a SHELXL molecule. [What does this mean?]
o Mouse bindings, consistency with MG. Can we drag using middle
mouse, instead of ctrl left mouse? Needs abstraction of state in
that function, I think.
o helix fitting overshoots. Try, amongst others, closed-monomer-works.map
o Fix the DNA/RNA names test (penelope gtk2 old-tests). 1hd
* see what cootbb says... Bill says add a thymine.
o consider making bonds to hydrogens thinner. A spike needed to
test for bonds split on thickness or colour most deeply.
o Problem SHELX .ins file, enable bonds to symmetry atoms?
o check for updates?
o push back the rotation centre (for hardware stereo mode) in the
viewport? [Mark Mayer 20080527].
o Revisit CCP4mg button
o Gtk2 coot: set the colour patch in the map properties and
symmetry molecule colouring (needs version 2.6). There is some
problem in the update, how do I set continuous updates on the
resulting colour chooser?
o (un)Label atoms in given atom selection
o More work on ligand bonding
Things with Cl etc,
O->P bonds
faster bonding with many molecules
o colour by B-factor CA mode
o Lasso (perhaps) active atoms to select atoms for R/Ting?
So that fragments of monomers can be moved independently
o Update python files
o Thymine in RNA: check string, "are you sure?" on finding a t. If
yes, sure add a Tr. Need to add an O2' somehow to the reference Tr.
o How about a post-swig command to add #ifdef USE_PYTHON around
coot_wrap_python.cc (or is it coot_wrap_python_pre.cc?)
Is that necessary now? In build-coot-fc4-gtk2,
coot_wrap_python.cc is generated and so is an practically empty
coot_wrap_python.lo
o rotamer-score function needs to be filled
* Done.
o "Find Waters" sometimes does not to put waters in what seems sensible
places - why is that?
* Done.
o Calculate NCS matrices from molecules created by
new_molecule_by_atom_selection()
o Check the distribution of selection of phi/psis from
random-phi-psi function matches a Ramachandran plot
o Randy's side-by-side frame drawing?
* Forget.
o Investigate communcation with PISA
* Done.
o "Fit ligand here" which gets a monomer then does a ligand search
based on the blob at the current position.
* Done.
o Non-bonded contacts. Can they be speeded up. What about nbcs
with Hydrogens. Are they good? Refine 50 residues and profile.
o Why does loop fitting fail on residue 96A of tutorial-modern.pdb?
o Make fit-loop work backward.
o Profile the bonding on reading in a ribosome fragment. 2 minutes?
Not good.
* It's not the bonding, it's in the mmdb read function.
o Make a demo script that downloads data and runs it - add it to
the package and make it available to run from extensions.
o Fit a ligand. Use write_connectivity to generate its hydrogens.
Use reduce and probe to make ligand interactions (and render them).
* Done.
o Display ligand diapoles using charges from cif file.
* Done.
o consider a function generator for dialog box of buttons. Because
we need a function that accepts args for close-dialog and one
that does not. A macro maybe.
o Rotate/Translate a whole protein (many chains)
* Done.
o When there is a non-square GL context, the axes become skewed.
Needs othogonalizing.
o Geometric distortions graph for alt confs - currently broken?
o Update stand-alone refinement program.
(Write a test for it?)
* Update done. Tried test. Problem in greg child process. Upgrade to
guile-1.8.3. Does that fix the greg child process problem? If not,
mail list. And give up. Check how greg behaves on compile/build -
it tests itself before install.
o The zooming in out out of a Ramachandran plot is inelegant.
Needs fixing.
o Integrate scripting functions into main documentation somehow
* Done.
o I want to be able to interupt those MR Extensions - not have to
wait.
* Done.
o When fitting waters in a low resolution(ish) map (from buccaneer
tutorial), the water were often placed in protein density - it was
missing the fact that the "water" density was connected to the
protein density - because we only look at the masked map.
(see bucca-tut on memory stick)
o Use LSQ not SSM for NCS ghost matrix.
(Make a speed test.)
* Done.
o *create* a molecule by symmetry, not (just) write it out.
Consider a dialog to Write/Create a symmetry molecule.
* Done.
o RNA backbone plot by connecting phosphates
* Done.
o NCS bone skeleton search - like ncs6d?. Can be punted, if needed.
o a test for write connectivity 1hd
* Don't know how to test this.
o Add to scripting layer: add-alt-conf that will work on the active
residue. Not sure if it should auto-accept. I guess not.
o rsync to bubbles test data.
* No need.
o "Add a NAG/XXX?" to this ASN. look at using spin-search. OK, a
new spin-search is needed, where we spin all of a given residue
round a bond specified in another residue. This will involved some
code refactoring. ::: 4
* Do it by searching against all ASN NAGs in the PDB.
o Can we have a regularize-residues (as in "sphere") function?
That would be cool for fixing molecular models. ::: 2
* Yes, done.
o Gtk2 coot: set the colour patch in the map properties and
symmetry molecule colouring (needs version 2.6). There is some
problem in the update, how do I set continuous updates on the
resulting colour chooser? ::: 2
o PRE: Minor irritation: if I display the molecule as CA atoms
only, clicking for naming or centering will still pick up the
invisible non-CA atoms. It would be Nice if it didn't. [Perhaps
he means CA + ligs mode?] ::: 2
* Done.
o Tips should have a "No more tips" checkbuttons (Coot behaves like
a proper program).
o Request from Antony Oliver: Put an indicator for the current
refinement map in (well, next to) the status bar. Consider greying
it out if the map is undisplayed.
o Request from JED: Make the EDS map getter have a cancel button.
And a progress bar ideally.
o We need a function that does a renumber and rechain at the same time
e.g. B 20-30 -> A 10-20
In such a case we can't renumber then change the chain id.
Use it in merge-solvent-chains, and make merge-solvent-chains not need
to renumber-waters first.
o EJD: I want to do a Ramachandran plot of only a selection of residues.
o EJD: I want the Ramachandran plot to be marked up if the atoms
have zero occupancy.
o Rebecca Vorhees(?) multiple residue ranges for the atom
selection for rotate/translate (first) and rigid body fit. And a
GUI to make the ranges.
* Done
o why is 'doc/c-interface_8h.texi' in the repository? It should
be generated.
o Make the Go To Atom button be in the toolbar [Maia Cherney]
o The Download from EDS needs an abort button (and thus downloaded
in a thread).
Punted from 0.6:
o Ingo K.: Ctrl left-mouse dragging sometimes does not work for alt
conf fragment residue. Can't reproduce. Punt. Needs checking
with Ingo. (He means refinement?)
o Does the window stay constant size (on something other than a
laptop) on start, exit, start exit cycling?
Priority: 6: Difficulty: 4 ::: 2
o Fix up mini-RSR so that it compiles properly. ::: 4
* Done.
o Put refine-zone and regularize-zone into the history. ::: 2
o consider making bonds to hydrogens thinner. A spike needed to
test for bonds split on thickness or colour most deeply. ::: 5
* Done.
o Delay the reading of coords, mtzs, maps until after ~/.coot etc
have been read (something like run_command_line_scripts()], see
handle_command_line_data(). [Pete Meyer] ::: 2
o Helix fitting overshoots - e.g.
1a02: place helix here at (9.2 36.6 28.3)
1env: place helix here - many places. Lots of errors.
3cjb_sigmaa at (-22.9451 0.2204 20.011) fail.
::: 4
o Markus Rudolf:
when updating to the latest gtk1 or gtk2 builds, we get this error:
Gtk-WARNING **: invalid cast from `GtkLabel' to `GtkContainer'
Gtk-CRITICAL **: file gtkcontainer.c: line 1119 (gtk_container_foreach): assertion `GTK_IS_CONTAINER (container)' failed.
gtk1 build 1855 works fine.
Baah. Can't reproduce. Needs to be followed up. get startup
script etc.
::: 1
o Add add rep of a residue. Change background to white. Rotate
view. Ugliness! ::: 2 [Erik Vogan]
* Done.
o Garib wants a function to move (symmetry-related) waters close to
the protein. ::: 4
* Done.
o Put the scripting window into the state file. How do we know if
the scripting window is open at end time? ::: 1
o Fixing atoms does not stop them from moving with
rotate/translate. Should it? Yes, I think ::: 1
o RNA/DNA backbone in symmetry.
* Done.
o For spin-searching the carbohydrate you need to give an atom spec
for the spin vector atoms.
o *create* a molecule by symmetry, not (just) write it out.
Consider a dialog to Write/Create a symmetry molecule. ::: 2
* You need to supply a RTop, not a string symmetry operator though.
We should have both, I suppose. Punt. Look at the
symm_card_composition_t class in coot-shelx.hh. Call it with the
passed string, and the loot at x_element, y_element, z_element (and
the frac_trans) to make a fractional matrix, which can be used in
new-molecule-by-symmetry.
o How about a "recover" .coot-recover file that contains the view
the saved pdb file, the molecule name (and whatever else is needed)
so that on a crash, coot can elegantly recover. That would be cool.
o ROT_TRANS_TYPE_MULTI_RANGE, so that we can make a "setup" of
rigid body refine at the scritping layer (currently rot/trans setup
is only done by clicking).
SCM rotate_translate_residue_ranges(int imol, SCM residue_ranges)
* Done.
o Env distances should have an "molecule number" attribute - when
that molecule is not displayed, not show the env distances.
* Done.
o Tim Fenn library thing.
Actually, this looks horrific
* Mostly done.
o Add a residue at residue number 2300 say and see if the sequence
view behaves OK.
o Phil Evans: can I set the NCS peer molecules myself so that NCS
modificiations are not set to molecules to which I think they don't
apply?
* I suppose so. clear-ncs-ghost-matrices and add-ncs-matrix. Or
simply change the homology_level (bad name for variable).
o make sure that PDB cif r2wousf.ent.gz (or some such, that you get
from the PDB works slickly as a cif file with sigmma maps).
o Residue Info window is not updated when an alt-conformation is
added [Miguel]
* Done.
o Need to fix up the baton build interface to add start up only
when there is a skeleton (or offer to do it).
o Put guile-gui and net-http into main Coot package - this makes the
Ubuntu/Fedora packaging a lot easier.
o Add an option to do sphere refinement in all molecule
Ramachandran refinement
o KH:
In baton build, make it work more clearly when starting
with no skeleton.
-> ask me to make a skeleton
o Stephen Graham: the NCS Master chain id on the NCS edits is
confusing. see email 2009/09/16
* Done.
o Validate ligand corresponds to dictionary. Are supposedly bonded
atoms within 3A or each other? Do the atom names match?
o in graphics_info_t::refine_residue() (or something) there is a
copy of the xmap out of the imol-refinement-map. Use a
reference. ::: 1
o JED: You should do RSR refinement on ligand fitting results to
make the score more meaningful. [Do it for the top n fits? ] ::: 6
o Make sulfurs yellow. At least optionally.
o Consider a "Validate" mode [checkbutton?] on reading coordinates
(or command line option). That displays Ramachandran plot, rotamer
analysis for the given molecule.
o "Fast Save" - save all models that have been changed to the
default name. ::: 2
* Done.
o SBASE or split up chemical component library and use (something
like?) get-monomer-from-dictionary()
o Steven Sheriff: PHE and TYR swaps (test_and_fix_PHE_TYR_nomenclature_errors())
should be written to console.
o put a "fix nomenclature errors" button in the rotamer graph.
o Steven Sheriff:: COOT is putting LINK records followed by SSBOND
records. The PDB standard is SSBOND records followed by LINK
records.
* Done.
0.6.1
27.5 dev points
o Check waters by difference map fails on Misty's waters. Data on
stick. ::: 3
o update guile :: 0.4
o Use libcurl to get URLs. It does proxies. Stop using nethttp.
::: 3
* Done.
o Quicksave: save all molecules (if they need saving) to default
names and save state. ::: 1
* Done.
o consider guile-lib's unit test, not greg.
::: 1
o Need a keybinding for "regularize these 3 residues". ::: 0.5
* Done.
o OXT in refinement (e.g. monomer-BCS.pdb) fails to reach
convergence. ::: 3
* Done.
o Baton-build mode needs to work better when starting with no
skeleton. ::: 1
o Can baton mode work when the skeleton runs out? ::: 3
o Fix the built-in help. ::: 1
o Find Waters: why does it miss some nice densities sometimes? ::: 4
* Done.
o Check hydrogens on ligands are generated by reduce? ::: 3
* Done.
o fit-waters should have a mode where bumps to protein atoms are
considered (not sphere refine - we don't want to move the protein
atoms). ::: 1
o the get_clash_score() in backrub_rotamer should work with a
(pre-generated) selection of residues - rather than the whole
molecule - which should speed things up a lot (especially for large
molecules). ::: 2
o HK: I want a function to set the refinement weight for me,
i.e. it should do a triple refine and look at the chi squareds.
Keep doing that with different weights until we get to 1.0. ::: 2
* Done.
o Make python coot work on CentOS 4. It does? Needs testing. ::: 2
* Done.
o I am looking at a symmetry-related part of the molecule. Take me
to the main molecule (try unapplying symmetry to get there).
::: 2
* Done.
o "Space" through waters. Delete a water. "space" recentres
where? Now do the same, but go through the waters backwards using
"shift space" - Ingo Korndoerfer ::: 1
* Done.
o Hydrogens should have thinner bonds. (Not half bonds - all grey
- more like molprobity/KING)
* Done.
o the chi-squared dialog should have "the worst geometric feature"
in the local refinement.
o Wiggly ligands for succrose in the CSH lysozyme data. Data on
stick. Maybe a dictionary issue ::: 2
o Rpath Library issues (Clemens message). ::: 2
o search for, download, update binary. Needs libcurl ::: 4
* Done.
o extend ^g mechanism to comprehend a 3-letter triple e.g. AGL (or lower
case) which refers to a position in the sequence. Look in displayed
molecules and go to the first one found. ::: 1
o check that the rama plot plots residues with alt confs. ::: 2
o sort chains should create a model by copying chains. that way
headers don't get lost. [JED bug] ::: 2
* Done?
o rework clipper.m4 so that it uses clipper-config, once
clipper-config is in place. ::: 2
o optimize_rotamer_by_atom_names() need to be thrown out and
rewritten. Use richardson rotamers (rotamer_probability_table) for
optimisation.
o alignment problems - Bob.
Putting the test-target.pir sequence of 3lhj onto 2z7l
(reference)
ISP-FE
LSRPFQ
Still an issue?
------
0.7 Priorities:
o Does Ca Zone -> Backbone crash? (or is that only trunk?) ::: 1
o read in 2Y0Z.pdb. Ugliness reading UNK from sbase.
o sphere refine doesn't work for alt confs.
o Airlie's ensemble_merged.pdb give bad bonding in 0.7-pre
o reading a cif from the PDB (e.g. 1X8B.cif) creates a molecule
with atom elements 1-char. Hence bonding fails.
Maybe also importing molecules from SBase.
* Done.
o change clipper macros to use clipper-config and not invent mmdb
and fftw, ccp4 libraries. clipper-config is broken (cctbx libs)
grr. ::: 3
o difference map (given previous model and new obs MTZ file, run
refmac no cyles to make a map, coot rigid-body per chain then
refmac to make phases for new model - get cell from passed MTZ
file, go to active site (passed value), create a view, pass 3
orthogonal views to be rendered by ccp4mg). Punted.
o consider roll up/collapse addition representation in Display
manager when they are not displayed. Punted. ::: 2
o Phil: I want to set in my ~/.coot file that all new molecules
will be opened in "colour by chain" mode (not just the ones that
I've already opened).
o Can you mutate residues in alt confs? BN ::: 3
* No. Should we be able? Yes, I think so.
o coordination number of waters validataion check (punted) ::: 5
* Done.
o draw surface within x A of a ligand
* Done.
o bonded_residues_conventional() need to check for other links in
the selection.
o check that SSBOND and LINK cards are valid on writing PDB.
o chemical component library interface (punted) ::: 4
o Generic Display Ojbect dialog should be scrollable (e.g. in use
with PISA interfaces).
o sphere-refine: turn on rama restraints for restraints from residue_vec.
make_link_restraints_by_linear() has
if (do_rama_plot_restraints)
add_rama_links(selHnd, geom);
make_link_restraints_from_res_vec() has
add_rama_links_from_res_vec(), but that is not filled.
need something like bonded_residues_from_res_vec(), but for
residue triples - returning 3 residues.
::: 3
o anisotropic atom radius. Punted ::: 1
o Environment distances turn off badly [JED]. Not sure if this is
a problem or how to fix it. Needs some thinking. Punted. ::: 1
o white background with ball and stick models. Punted ::: 4
* Done.
o Put "Modified Residue/Other" button in Mutate dialog that fires
up the "Replace Residue" dialog - or something like that.
o Rotate/Translate on dsDNA (for example)
* Done.
o Move (symmetry-related) waters around protein (or has this been
done by now?)
* Done.
o CA (or CA + ligs?) mode, edit bond colours -> Changes the colour
of the first chain only. ::: 1
* Done.
o Rotation for add terminal residue. hari jayaram & Donald Raymond
::: 2
* Bleugh. How about a keybinding that fires up the R/T dialog mode
for the newly added residue?
o mutate-by-overlap: if you have already loaded a molecule with a
single residue with name XXX and you have read in a dictionary
entry for XXX, then coot should use that. [ Tickle, 20090723] ::: 3
* Done.
o to make the rotamer probabilites smooth, FFT them like
Otwinowski's Ramachachandran plots. FFTW in mult-dimentions. Hmm.
o (consider) Luca Jovine: I want to do sphere regularization ::: 2
* Done.
o (consider) Add/generate HELIX and SHEET PDB header info. ::: 3
o consider changing auto-open behaviour, as Randy Read suggests.
Or perhaps like Kevin suggests: prefix.F and prefix.phi
::: 3
o "Quick Bumps"
o Find nomenclature errors on reading coordinates file and give a
dialog to fix if necessary
o "Flip" chirality restraint
* Done.
o Put Sphere Refinement in modelling toolbar
* Done.
o Bond ligand by dictionary
* Done.
o symmetry-related pointer distances?
* Done.
o handle_command_line_data() should happen in c_inner_main(), after
reading ~/.coot (and other scripts, perhaps?). Which means, I
think, that graphics_info_t:: needs a static copy of the cld.
o "click - click" to add a LINK (and LINK record)
* Done.
o Ramachandran plots don't update on "undo"? Punt.
*Maybe done, needs checking.
o Rotamer plot doesn't update on sidechain 180? Punt.
o Martyn: http://2dx.org/documentation/mrc-software/mrc-documentation
"23 ISPG space group number 0 or 1 (default=0)".
If spacegroup is 0, put the map into an nxmap. ::: 6
o when running from the "wrong" directory, do a better job at
letting the user know there is a problem (an informative dialog,
let's say) when running (say) search monomer library and pressing
on a returned button. ::: 1
o residues in DNA from modern PDB files is DG, DA, DC, DT. Need
to map to refmac name, restraints don't work.
* Done.
* The correct solution is to generate a dictionary for DG, DA
etc from that GD.cif (Gd) (etc) as they are read in. Note that in
DT, C5M (in the dictionary) become C7 (new PDB coordinate
format/convention).
* Done.
o Phil Evans: "the Extensions->NCS->Copy NCS residue range only
seems to work if the master chain is the same as that given in the
NCS ghost control. Otherwise nothing happens and there's no error
message."
* Added error message.
We need a function to return the NCS masters of a given molecule
(deep inspection of the target chains of the ghosts, I guess).
Return a SCM: #f or a list of chain-ids (hopefully, just one
item).
* Done.
o update probe dots (probe-local-sphere) should do a merge with
already existing dots - removing the overlaping dots.
* Done?
o in simple_restraint::minimize() should we return traffic lights
when the result has not terminated correctly? Currently the return
value from chi_squareds() is not saved (and returned).
* Done.
o Add a NAG to this ASN (or ARG (less common)) (this is N-linked).
Also consider O-link (on a SER, THR, TYR). Examine good N-linked
NAGs in PDB structures and find the chi1, chi2, glycosylation link
torsion angle. Use these to same from. JB
o I want to add a residue that has insertion code (e.g. add to
residue 60 and residue 61 already exists). JB.
o Sue Roberts: when generating sfs from cif
(run-refmac-for-phases), make it so that refmac doeesnt check the
geometry of the ligand (or so) first. Just generate sfs! talk to
garib about how to do that.
o internal: c-interface map functions should be in
c-interface-maps.cc
o consider an option for refinement post-ligand. Consider a
command-line tool for this (shell script maybe).
o Kevin NX map code for EM maps [11 Aug 2010: nxmap]
o torsion on a NAD work (fix the dictionary)?
* Pending reply from Garib.
o clipper::Skeleton_basic::Neighbours neighb(xmap, 0.25, 1.75); // 3x3x3 cube, not centre
this is not true: needs checking where such neighbours are set
we pass square limits, i.e. 0.5 and 3.1 for 3x3x3 cube, not centre