At least for my resolutions, the measure tool renders its text outside the view. So I can see the highlighted atoms, but not the actual measurement.

Reported by: @ghutchis

Currently, if I drag files to Avogadro on a Mac to open them, I'm left with one empty window. (Also, all the windows are in exactly the same spot.)

The code in main.cpp and application.cpp should take care of this, but it's not clear where the extra window comes -- it appears to be the first window created.

Also, the code in application.cpp could (in principal) be combined with MainWindow::openFile(filename).

Reported by: @ghutchis

The current "optimize geometry" extension provides little feedback of what's going on or how long the task will take.

Ideally, this should take place in a separate thread and provide some sort of progress indicator. (Also, ideally, there should be a configuration dialog to adjust the parameters of the optimization.)

Reported by: @ghutchis

Since the recent changes bringing renderOpaque, renderTransparant, overlays, etc., the LabelEngine triggers some bugs:

1. When LabelEngine is active, the yellow sphere of the navigatetool is no longer transparent.
2. When LabelEngine is active, only one of the molecules in a UnitCell gets rendered, the others are hidden. Moreover, the labelengine shows a transparency problem in that case.

I have added qDebug() to check the glPushMatrix/glPopMatrix calls in TextRenderer, and they look just fine. Therefore I suppose this might be a problem in the new "overlay" system (as LabelEngine is flagged as an overlay), which is why I assign this bug to you, Donald.

Reported by: benoitjacob

Settings -> Docks menu does not contain an item for the Engines dock.

Reported by: dcurtis3

Qt 4.3.1, r656

Steps to reproduce:

1. Open Avogadro
2. In the "Engine Configuration" switch to the "Primitives" Tab
3. Click on the rightmost button (the green arrow).

It crashes. Note that I don't have any engines in the white widget above.

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1225537840 (LWP 5214)]
0x08068f10 in Avogadro::EngineSetupWidget::addAll ()
(gdb) bt
#0 0x08068f10 in Avogadro::EngineSetupWidget::addAll ()
#1 0x0806921d in Avogadro::EngineSetupWidget::qt_metacall ()
#2 0xb74e2081 in QMetaObject::activate () from /usr//lib/libQtCore.so.4
#3 0xb74e2390 in QMetaObject::activate () from /usr//lib/libQtCore.so.4
#4 0xb7d60ec1 in QAbstractButton::clicked () from /usr//lib/libQtGui.so.4
#5 0xb7b4c969 in QButtonGroup::id () from /usr//lib/libQtGui.so.4
#6 0xb7b4d869 in QAbstractButton::focusInEvent () from /usr//lib/libQtGui.so.4
#7 0xb7b4da90 in QAbstractButton::mouseReleaseEvent () from /usr//lib/libQtGui.so.4
#8 0xb7c06f5c in QToolButton::mouseReleaseEvent () from /usr//lib/libQtGui.so.4
#9 0xb78ccfb2 in QWidget::event () from /usr//lib/libQtGui.so.4
#10 0xb7b4e133 in QAbstractButton::event () from /usr//lib/libQtGui.so.4
#11 0xb7c06874 in QToolButton::event () from /usr//lib/libQtGui.so.4
#12 0xb7888cf0 in QApplicationPrivate::notify_helper () from /usr//lib/libQtGui.so.4
#13 0xb788f027 in QApplication::notify () from /usr//lib/libQtGui.so.4
#14 0xb74d0ecb in QCoreApplication::notifyInternal () from /usr//lib/libQtCore.so.4
#15 0xb78dea86 in QApplication::x11ProcessEvent () from /usr//lib/libQtGui.so.4
#16 0xb78de1a3 in QApplication::x11ProcessEvent () from /usr//lib/libQtGui.so.4
#17 0xb7900ddb in QX11Info::copyX11Data () from /usr//lib/libQtGui.so.4
#18 0xb6fafde2 in g_main_context_dispatch () from /opt/gnome/lib/libglib-2.0.so.0
#19 0xb6fb2e1f in g_main_context_prepare () from /opt/gnome/lib/libglib-2.0.so.0
#20 0xb6fb3385 in g_main_context_iteration () from /opt/gnome/lib/libglib-2.0.so.0
#21 0xb74f2808 in QEventDispatcherGlib::processEvents () from /usr//lib/libQtCore.so.4
#22 0xb7900bc5 in QX11Info::copyX11Data () from /usr//lib/libQtGui.so.4
#23 0xb74d0408 in QEventLoop::processEvents () from /usr//lib/libQtCore.so.4
#24 0xb74d051c in QEventLoop::exec () from /usr//lib/libQtCore.so.4
#25 0xb74d25d8 in QCoreApplication::exec () from /usr//lib/libQtCore.so.4

---Type to continue, or q to quit---
#26 0xb7888407 in QApplication::exec () from /usr//lib/libQtGui.so.4
#27 0x0806d2a7 in main ()

Reported by: @cniehaus

The Engine list gets updated when you change a view but it doesn't get properly updated when you close a view and the next view is selected.

Reported by: dcurtis3

build C-C, add H, change one H to C, add H (no H's are added the second time). It looks like this is more related to the way the OpenBabel ::AddHydrogens is performing but somehow needs to get fixed.

Reported by: dcurtis3

The quit command on Mac is inconsistent. If you quit via the dock, windows will be requested to save (via closeEvent).

If you quite from the toolbar or menu, no closeEvent is sent.

I think this may be a Trolltech bug, but will post to qt-interest to check.

This bug in Avogadro is a reminder to fix our behavior.

Reported by: @ghutchis

The AddAtomDrawCommand takes as a parameter a glWidget. This isn't needed by the Command itself (needs to be removed) but it brings up an interesting situation; undo/redo commands related to a GLWidget must somehow be delt with when the GLWidget they are performed on get removed.

Reported by: dcurtis3

On a white background, the anti-aliased text render (i.e. for the Debug engine) looks really lousy. I think the main problem is that the anti-aliasing is a bit too much, so you see a lot of grey from the outline.

This is a pretty minor problem, but I wanted to get it in the list anyway.

Reported by: @ghutchis

The draw tool has a mode where you can change the element by clicking on an existing atom.

This does not generate an undo command (change atom?).

This also does not update the painting in the GLWidget. Only creating a new atom (or anything else) will cause an update.

Reported by: @ghutchis

Hi,

I have some protein file that I use for testing; in the default viewpoint with maximized window I used to get 8 FPS and since some time I only get 3.5 FPS. I think that change happened approximately at the time when threading was introducted, or maybe when renderOpaque/renderTransparent were introduced.

Moreover, frustum culling does no longer seem to help performance. With that same molecule, when using a viewpoint from which only a few atoms were visible, I used to get more than 40 FPS. Now I can't get more than 4.5 FPS.

Some things to investigate:
-- is blending enabled when it's not needed (opaque objects)?
-- is backface culling disabled when it doesn't have to be disabled (opaque objects) ?
-- is some operation being performed on all atoms/bonds before frustum culling gets a chance to cull them out? Currently, frustum culling is done in the Painter methods (see the check with the dot product). Maybe it needs to operate somewhere upstream instead?

Reported by: benoitjacob

Hey...

Open a file, use the bond centric manipulation tool. Change the value on the snap-to-angle spinbox. Crash.

100% reproducable.

Qt 4.3.1, todays SVN (r654),

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1225673008 (LWP 7144)]
0xb7345a4e in Eigen::VectorBase<double, Eigen::Vector<double, 3> >::readArray ()
from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
(gdb) bt
#0 0xb7345a4e in Eigen::VectorBase<double, Eigen::Vector<double, 3> >::readArray ()

from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#1 0xb7345aa9 in Eigen::Vector<double, 3>::Vector () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#2 0xb6a8159a in Avogadro::BondCentricTool::snapToAngleChanged ()

from /home/kde4/build/avo/libavogadro/src/tools/libbondcentrictool.so
#3 0xb6a8470c in Avogadro::BondCentricTool::qt_metacall ()

from /home/kde4/build/avo/libavogadro/src/tools/libbondcentrictool.so
#4 0xb74c1081 in QMetaObject::activate () from /usr//lib/libQtCore.so.4
#5 0xb74c1b82 in QMetaObject::activate () from /usr//lib/libQtCore.so.4
#6 0xb7d437f3 in QSpinBox::valueChanged () from /usr//lib/libQtGui.so.4
#7 0xb7bc0049 in QDoubleSpinBox::QDoubleSpinBox () from /usr//lib/libQtGui.so.4
#8 0xb7b31d45 in QAbstractSpinBox::minimumSizeHint () from /usr//lib/libQtGui.so.4
#9 0xb7b335ae in QAbstractSpinBox::stepBy () from /usr//lib/libQtGui.so.4
#10 0xb7b30637 in QAbstractSpinBox::qt_metacast () from /usr//lib/libQtGui.so.4
#11 0xb7b3282b in QAbstractSpinBox::mousePressEvent () from /usr//lib/libQtGui.so.4
#12 0xb78ac1c5 in QWidget::event () from /usr//lib/libQtGui.so.4
#13 0xb7b32934 in QAbstractSpinBox::event () from /usr//lib/libQtGui.so.4
#14 0xb7bbed46 in QSpinBox::event () from /usr//lib/libQtGui.so.4
#15 0xb7867cf0 in QApplicationPrivate::notify_helper () from /usr//lib/libQtGui.so.4
#16 0xb786e027 in QApplication::notify () from /usr//lib/libQtGui.so.4
#17 0xb74afecb in QCoreApplication::notifyInternal () from /usr//lib/libQtCore.so.4
#18 0xb78bda86 in QApplication::x11ProcessEvent () from /usr//lib/libQtGui.so.4
#19 0xb78bd1a3 in QApplication::x11ProcessEvent () from /usr//lib/libQtGui.so.4
#20 0xb78dfddb in QX11Info::copyX11Data () from /usr//lib/libQtGui.so.4
#21 0xb6f8ede2 in g_main_context_dispatch () from /opt/gnome/lib/libglib-2.0.so.0
#22 0xb6f91e1f in g_main_context_prepare () from /opt/gnome/lib/libglib-2.0.so.0

---Type to continue, or q to quit---
#23 0xb6f92385 in g_main_context_iteration () from /opt/gnome/lib/libglib-2.0.so.0
#24 0xb74d1808 in QEventDispatcherGlib::processEvents () from /usr//lib/libQtCore.so.4
#25 0xb78dfbc5 in QX11Info::copyX11Data () from /usr//lib/libQtGui.so.4
#26 0xb74af408 in QEventLoop::processEvents () from /usr//lib/libQtCore.so.4
#27 0xb74af51c in QEventLoop::exec () from /usr//lib/libQtCore.so.4
#28 0xb74b15d8 in QCoreApplication::exec () from /usr//lib/libQtCore.so.4
#29 0xb7867407 in QApplication::exec () from /usr//lib/libQtGui.so.4
#30 0x0806d2a7 in main ()

Reported by: @cniehaus

The various warnings (e.g., to save before quitting) do not use the Qt::Sheet property, as typically used by native Mac applications.

http://doc.trolltech.com/qq/qq18-macfeatures.html

Reported by: @ghutchis

• Opening *.smi files produces a garbled "View", activating engine "Debug" additionaly segfaults avogadro.

Reported by: soc88

Start with a molecule with some existing hydrogens (e.g., an imported crystal structure or PDB file), like the attached file. Add hydrogens. Try "undo" and all hydrogens are removed, including the original ones.

In short, for files with some existing hydrogens, "Add Hydrogens" and "Remove Hydrogens" are not perfect redo/undo pairs, since you will not get back to the original state.

Reported by: @ghutchis

Right now there is no gas phase option. Only water, but the corresponding
keywords are not it the input file.

When I build C-C-N and add hydrogens, I get CH3-CH2-NH3. That's fine, but
when I open the GAMESS input, the input says scftyp=rohf, mult=2 (i.e.
doublet); while the menu says singlet. Assuming the charge is neutral, the
input is actually correct. Another option is cation, singlet, but when I
try this the ROHF does not go away as it should.

Reported by: dcurtis3

On the Mac OSX port the close buttons quits the program rather than clearing the current molecule.

Reported by: dcurtis3

The current about box doesn't even include the URL for the Avogadro homepage. Better yet would be an active hyperlink.

Reported by: @ghutchis

Need to make it so the engines are properly labeling bonds, can render selection feedback on bonds and that the selection engine actually selects them.

Reported by: dcurtis3

When you choose the "quit" menu item on the Mac, the program quits immediately, rather than prompting to save any unsaved changes in windows.

Reported by: @ghutchis

The camera's project function is projecting into a co-ordinate system with 0,0 at the bottom left and the y axis going up instead of having 0,0 at the top left and the y axis going down.

Reported by: rbraith

Load a CML file.

Add for example 8 Carbon atoms to a Oxygen atom (I know in real life this doesn't work...). Now optimzie the geometry. Works.

Now add the hydrogens with the menu-option and optimize again. After about 2 minutes with 60-80% consumption of my memory I killed Avogadro.

Reported by: @cniehaus

If I use the manipulatetool or navigatetool and click on an atom while labels are displayed, the "extra" transparent sphere (in red or yellow) from the tool does not properly overlay the label.

There is a small semi-circular region which does not reflect the red or yellow color. This is best illustrated in the attached screenshot from Mac OS X.

Reported by: @ghutchis

Windows is having some problem detecting my mouse scroll up and down. This didn't happen before. I believe it's something with 4.3.1 Will have to examine more later and put in some debug code to see what's happening with the mouse.

Reported by: @milkypostman

Auto Rotation Tool

A red line can be drawn in the View Widget to setup the rotation.
The red line is sometimes drawn behind some atoms, sometimes in front of them, depending on rotation and size of molecules.
(Don't know if that's a feature or bug)

Reported by: soc88

Currently, updateGeometry() only tracks single molecules. The code needs an update to properly handle unit cells. A new SVN update will have the logic, but not necessarily the correct geometric calculation.

Unit cells add translation, starting at the origin, so the center should be at (a + b + c) / 2, although no atom may appear at this point in space. (The a, b, and c vectors are the sides of the parallelepiped defining the unit cell.)

The radius should be the magnitude of this vector from 0,0,0 to the center.

Benoit, could you check this? I'm not sure what needs to happen in updateGeometry -- more documentation or comments would be realyl welcome.

Thanks!

Reported by: @ghutchis

If the user has selected a set of atoms, the hydrogen addition or removal should only operate on those selected atoms. This allows "partial hydrogenation." :-)

Reported by: @ghutchis

When I make a Methane molecule and tell your program to optimize the geometry, it crashes.

Reported by: *anonymous

Each thread of Avogadro needs a new instance of a tool so that when you select it there is a configuration dialog. Else each time you open a new thread "New" the tool dialog gets a new owner. If the newly created thread is desroyed, that widget gets destroyed too.

Reported by: dcurtis3

It appears that the Left Click and Right Click buttons don't properly perform on the Mac OSX port. I believe this is a known issue but am marking it down.

Reported by: dcurtis3

There's no way to use a draw tool to erase a bond (but leave the atoms intact).

Reported by: @ghutchis

If you create two views and close the first then perform Edit->Select None, there is a segfault. The bug is because the closeView() function is not properly setting the new widget.

Reported by: dcurtis3

Since the threading-branch was merged into trunk Avogadro no longer starts.

I already reported this by mail:

http://sourceforge.net/mailarchive/forum.php?thread_name=c048b1c20707210441s144e9d3bg9443a3d12e93b852%40mail.gmail.com&forum_name=avogadro-devel

I am using OpenBabel 2.1.1, tested this with both CMake 2.4.6 and 2.4.7, using a patched Qt 4.3.0 (patches from the snapshorts to 4.3.1 as provided by OpenSUSE). All other applications (also those using threads in Qt) work without issues.

Here is what strace tells me:

chdir("/home/kde4/build/avo") = 0
stat64("/usr/lib/qt4/plugins/inputmethods/libqimsw-multi.so", {st_mode=S_IFREG|0755, st_size=27444, ...}) = 0
stat64("/usr/lib/qt4/plugins/inputmethods/libqimsw-multi.so", {st_mode=S_IFREG|0755, st_size=27444, ...}) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
open("/home/kde4/.config/Trolltech.conf", O_RDONLY|O_LARGEFILE) = 8
close(8) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
stat64("/etc/settings/Trolltech.conf", 0xbffdd350) = -1 ENOENT (No such file or directory)
stat64("/etc/settings/Trolltech.conf", 0x80e3878) = -1 ENOENT (No such file or directory)
stat64("/home/kde4/build/avo/avogadro/src/inputmethods/.", 0x80e3740) = -1 ENOENT (No such file or directory)
lstat64("/home/kde4/build/avo/avogadro/src/inputmethods/.", 0xbffdd730) = -1 ENOENT (No such file or directory)
stat64("/home/kde4/kde/lib/kde4/plugins/inputmethods/.", 0x80e3740) = -1 ENOENT (No such file or directory)
lstat64("/home/kde4/kde/lib/kde4/plugins/inputmethods/.", 0xbffdd730) = -1 ENOENT (No such file or directory)
write(7, "\24\0\6\0D\0\0\0\27\0\0\0\0\0\0\0\0\0\0\0\0 \0\0", 24) = 24
read(7, "\1\10z\0G\20\0\0\37\0\0\0\0\0\0\0\33A\0\0\0\0\0\0\0\0\0"..., 32) = 32
readv(7, [{"*AxeText.Translations:\t#override"..., 16667}, {"\0", 1}], 2) = 16668
writev(7, [{"b\0\6\0\17\0\0\0", 8}, {"XInputExtension", 15}, {"\0", 1}], 3) = 24
read(7, "\1\322{\0\0\0\0\0\1\221_\250\0\20\0\0\0\0\0\0\0\0\0\0\0"..., 32) = 32
futex(0x80cb468, FUTEX_WAIT, 2, NULL

I have no idea how to debug this any further so please guide me.

Reported by: @cniehaus

If a molecule has an increasing number of atoms "Tools"->"optimize geometry" tends to fail more often, producing a black, non-usable "View". The Atoms are not visible anymore.

C O N J U G A T E G R A D I E N T S

STEPS = 100

STEP n E(n) E(n-1)

1    1370.881    5406.779
2    1075.939    1370.881
3     870.825    1075.939
4     803.394     870.825
5     784.854     803.394
6     761.331     784.854
7     747.684     761.331
8     732.933     747.684
9     728.820     732.933

10 720.572 728.820
...
53 682.817 682.869
54 682.780 682.817
55 682.754 682.780
56 682.731 682.754
57 nan 682.731 <===HERE!
58 nan nan
59 nan nan
...
97 nan nan
98 nan nan
99 nan nan

100 nan nan

Reported by: soc88

Particularly on my Mac, when I launch, the first painting of the GLWidget yields a "stretched" look (see attachment).

Resizing the window results in a normal look to the render.

Perhaps the initial GLWidget (or somewhere along the render chain) is assuming a particular window size? Avo has saved my preference for a large window.

Reported by: @ghutchis

If you build C-C and add H, the H's are added in an eclipsed position (i.e. H-C-C-H angle is 0) but the lowest energy should be staggered (H-C-C-H angle 60). This is also not fixed in the geometry optimization. This also happens for larger molecules like C-C-C-C for some bonds.

Reported by: dcurtis3

If you have an atom selected and then delete it, doing a "Select None" will cause a segfault.

Reported by: dcurtis3

cmake/modules/FindOpenBabel2.cmake tells "Could NOT find OpenBabel2", which is not true if Openbabel 2.0 is installed (it's just not new enough). You should fix this to output the real issue.

I'm further suprised by the Windows registry path: HKEY_CURRENT_USER\SOFTWARE\OpenBabel\ 2.0.2. If 2.1 is requirered, is this path correct?

Further the file (and another too) refers to COPYING-CMAKE-SCRIPTS, which is not shipped with the source.

Reported by: dleidert

If I close the first MainWindow opened (e.g., on Mac with multiple windows open), the views in second window goes blank.

This can be fixed by creating a new view, and then closing the existing "view 0."

It's not clear why the view goes to black. It also doesn't affect other windows if you have >2 windows open when you close the first.

Reported by: @ghutchis

At least on my Mac, the updated text render does not appear. No text is rendered.

I'd take the slightly lower quality one over nothing at all. :-)

Reported by: @ghutchis

On the Mac, in the current SVN trunk, the "Preferences" command in the global Avogadro application menu pulls up the Ghemical force field setup dialog.

Instead, this should be the command which ends up on the Settings menu.

Reported by: @ghutchis

Selections are (mostly) stored in the GLWidget view. Selection of residues is not always updated properly, particularly across new views.

The selection code should uniformly use the GLWidget selection property and eliminate the selection information in the Primitive classes.

Reported by: @ghutchis

"Open File"-Dialog doesn't remember last directory.

The "Open File"-Dialog should show the last directory, so people don't have to navigate through their directories again.

Reported by: soc88

Ctrl+C doesn't work in "Messages" tab, causes Segmentation fault.
Rightclick->"Copy (Ctrl+C)" works, though.

Reported by: soc88

If I use the manipulate tool and move an atom, there's no undo/redo possible.

Reported by: @ghutchis

- while performing geometry optimizations:

("avogadro")
Found Engine: "Axes" - "Renders x, y and z axes"
Found Engine: "Dynamic Ball and Stick" - "Renders primitives using Balls (atoms) and Sticks (bonds). Includes demonstration of dynamic rendering based on distance from camera"
Found Engine: "Debug Info" - "Renders debug information"
Found Engine: "Label" - "Renders primitive labels"
Found Engine: "Ribbon" - "Renders residues as ribbons"
Found Engine: "VdW Sphere" - "Renders atoms as Van der Waals spheres"
Found Engine: "Stick" - "Renders as Cylinders"
Found Engine: "Wireframe" - "Wireframe rendering"
"libautorotatetool.so"
Found Tool: "AutoRotate" - "Auto Rotation Tool"
"libbondcentrictool.so"
Found Tool: "BondCentric" - "Bond Centric Manipulation Tool"
"libclickmeasuretool.so"
Found Tool: "ClickMeasure" - "Click to Measure Tool"
"libdrawtool.so"
Found Tool: "Draw" - "Draws Things"
"libmanipulatetool.so"
Found Tool: "Manipulate" - "Manipulation Tool"
"libnavigatetool.so"
Found Tool: "Navigate" - "Navigation Tool"
"libselectrotatetool.so"
Found Tool: "Select/Rotate" - "Selection and Rotation Tool"
SearchPath: "/usr/local/lib/avogadro/extensions"

Found Extension: "GAMESS" - "GAMESS Input Deck Generator"
Object::connect: Parentheses expected, slot Avogadro::GamessExtension::dockWidgetDestroyed
ForceFieldDialog::ForceFieldDialog()

Found Extension: "Ghemical" - "Ghemical Plugin"
Found Extension: "H2Methyl" - "H2Methyl Plugin"
Found Extension: "Hydrogens" - "Hydrogens Plugin"
Found Extension: "SMARTS" - "SMARTS Plugin"
Found Extension: "UnitCell" - "Unit Cell Parameters Plugin"
createObjects()
QObject::connect: Cannot queue arguments of type 'QTextCursor'
(Make sure 'QTextCursor' is registered using qRegisterMetaType().)
*** glibc detected *** avogadro: double free or corruption (!prev): 0x0000000001a4a250 ***
======= Backtrace: =========
/lib/libc.so.6[0x2b302c033b0a]
/lib/libc.so.6[0x2b302c0356d8]
/lib/libc.so.6(realloc+0x129)[0x2b302c037979]
/usr/lib/libQtGui.so.4[0x2b30285e191a]
/usr/lib/libQtGui.so.4[0x2b30285e5410]
/usr/lib/libQtGui.so.4[0x2b30285e570b]
/usr/lib/libQtGui.so.4[0x2b3028601d15]
/usr/lib/libQtGui.so.4[0x2b3028550829]
/usr/lib/libQtGui.so.4(_ZNK11QTextEngine9shapeTextEi+0x272)[0x2b302856156e]
/usr/lib/libQtGui.so.4(_ZNK11QTextEngine5shapeEi+0x116)[0x2b3028562a16]
/usr/lib/libQtGui.so.4(_ZN9QTextLine13layout_helperEi+0x2da)[0x2b302856d306]
/usr/lib/libQtGui.so.4(_ZN9QTextLine12setLineWidthEd+0x75)[0x2b302856e0d1]
/usr/lib/libQtGui.so.4[0x2b30285a1b4c]
/usr/lib/libQtGui.so.4[0x2b30285a3ea0]
/usr/lib/libQtGui.so.4[0x2b30285a8314]
/usr/lib/libQtGui.so.4[0x2b30285a8a23]
/usr/lib/libQtGui.so.4[0x2b30285a8af7]
/usr/lib/libQtGui.so.4[0x2b30285a95f4]
/usr/lib/libQtGui.so.4[0x2b302858b7be]
/usr/lib/libQtGui.so.4(_ZN11QTextCursor12endEditBlockEv+0x4f)[0x2b30285b2bcf]
/usr/lib/libQtGui.so.4(_ZN12QTextControl6appendERK7QString+0x139)[0x2b3028551e4f]
/usr/lib/libQtGui.so.4(_ZN9QTextEdit6appendERK7QString+0x58)[0x2b302876a05c]
/usr/local/lib/avogadro/extensions/libghemicalextension.so(_ZN8Avogadro14GhemicalThread3runEv+0x4da)[0x2aaaad0d62c2]
/usr/lib/libQtCore.so.4[0x2b302a7a1a12]
/lib/libpthread.so.0[0x2b302ad44317]
/lib/libc.so.6(clone+0x6d)[0x2b302c095ccd]
======= Memory map: ========
00400000-0045e000 r-xp 00000000 08:03 544236 /usr/local/bin/avogadro
0065d000-0065f000 rw-p 0005d000 08:03 544236 /usr/local/bin/avogadro
0065f000-01f5b000 rw-p 0065f000 00:00 0 [heap]
40000000-40001000 ---p 40000000 00:00 0
40001000-40801000 rwxp 40001000 00:00 0
40801000-40802000 ---p 40801000 00:00 0
40802000-41002000 rwxp 40802000 00:00 0
41002000-41003000 ---p 41002000 00:00 0
41003000-41803000 rwxp 41003000 00:00 0
41803000-41804000 ---p 41803000 00:00 0
41804000-42004000 rwxp 41804000 00:00 0
2aaaaaaab000-2aaaaaab3000 r-xp 00000000 08:03 35668 /usr/lib/qt4/plugins/imageformats/libqgif.so
2aaaaaab3000-2aaaaacb2000 ---p 00008000 08:03 35668 /usr/lib/qt4/plugins/imageformats/libqgif.so
2aaaaacb2000-2aaaaacb3000 rw-p 00007000 08:03 35668 /usr/lib/qt4/plugins/imageformats/libqgif.so
2aaaaacb3000-2aaaaacbf000 r-xp 00000000 08:03 35682 /usr/lib/qt4/plugins/imageformats/libqjpeg.so
2aaaaacbf000-2aaaaaebe000 ---p 0000c000 08:03 35682 /usr/lib/qt4/plugins/imageformats/libqjpeg.so
2aaaaaebe000-2aaaaaebf000 rw-p 0000b000 08:03 35682 /usr/lib/qt4/plugins/imageformats/libqjpeg.so
2aaaaaedc000-2aaaaaefd000 r-xp 00000000 08:03 7205 /usr/lib/libjpeg.so.62.0.0
2aaaaaefd000-2aaaaaffd000 ---p 00021000 08:03 7205 /usr/lib/libjpeg.so.62.0.0
2aaaaaffd000-2aaaaaffe000 rw-p 00021000 08:03 7205 /usr/lib/libjpeg.so.62.0.0
2aaaaaffe000-2aaaab005000 r-xp 00000000 08:03 38729 /usr/lib/qt4/plugins/imageformats/libqmng.so
2aaaab005000-2aaaab204000 ---p 00007000 08:03 38729 /usr/lib/qt4/plugins/imageformats/libqmng.so
2aaaab204000-2aaaab205000 rw-p 00006000 08:03 38729 /usr/lib/qt4/plugins/imageformats/libqmng.so
2aaaab222000-2aaaab29c000 r-xp 00000000 08:03 7250 /usr/lib/libmng.so.1.1.0.9
2aaaab29c000-2aaaab39b000 ---p 0007a000 08:03 7250 /usr/lib/libmng.so.1.1.0.9
2aaaab39b000-2aaaab3a0000 rw-p 00079000 08:03 7250 /usr/lib/libmng.so.1.1.0.9
2aaaab3a0000-2aaaab3d2000 r-xp 00000000 08:03 82533 /usr/lib/liblcms.so.1.0.16
2aaaab3d2000-2aaaab5d2000 ---p 00032000 08:03 82533 /usr/lib/liblcms.so.1.0.16
2aaaab5d2000-2aaaab5d4000 rw-p 00032000 08:03 82533 /usr/lib/liblcms.so.1.0.16
2aaaab5d4000-2aaaab5d6000 rw-p 2aaaab5d4000 00:00 0

2aaaab5d6000-2aaaab5db000 r-xp 00000000Aborted

Reported by: soc88

After switch to glwidget based selection, the paste command does not select the new atoms for manipulation.

This would be extremely handy.

Reported by: @ghutchis

All atoms have some minor pixel-sized graphical errors.

(Don't know too much about C++/OpenGL, so i can't provide any further information at the moment.)

Reported by: soc88