Tracker log

An overview of recent activity in the tracker.

Richard Gildea added a new response to »Content Error in help for Tool Bar Model«:

Fixed.

Issue state: Unconfirmed → Resolved.
Responsible manager: (UNASSIGNED) → rgildea.
Added 50 minute(s) ago.

New issue »Content Error in help for Tool Bar Model« added by Bruce Noll

The info text for the atom type in the Toolbox Work refers to *red* atom labels when the number in model do not match the number in the formula. It continues to state that the labels will be *red* if the formula matches model. This second instance of *red* should be *green*. I copied the offending text below.

Also, "problems" is misspelled "problmes"on the Olex2 home page for v1.1-beta.


Toolbar Model
This is a collection of three basic tools needed for model building.
Assign Atom Types All atom types that are currently in your formula are represented as a small button. You can click on one of these buttons and will go into an atom type assignment mode for this particular atom type. Atoms you click subsequently will become that atom type. Alternatively, you can make a selection of atoms first, and then click the atom type symbol. The buttons will appear red, if there are fewer atoms of that type in your model compared to the formula you have initially given. They turn red if the numbers do agree.
>> name sel C
>> mode name C

Added 15 hour(s) ago.

Oleg Dolomanov added a new response to »Groups? Broken? Possibly?«:

Right, http://www.olex2.org/content/olex2-bugs/273 is a perfect example for this crash. Fixed in source.

Issue state: Unconfirmed → Confirmed.
Responsible manager: (UNASSIGNED) → Oleg.
Added 9 day(s) ago.

Oleg Dolomanov added a new response to »WBOX generated half of the necessary box«:

OK, in this particular case one the molecule lies in one of the planes defined by the inertia tensor but the algorithm would only investigate the side of the plane on which it lies, and since the machine zero is never machine zero, only half of the cases would be investigated, leading to possible incorrect result to 'very' flat molecules... Will be fixed in next update.

Issue state: Confirmed → In progress.
Severity: Medium → Important.
Added 9 day(s) ago.

Oleg Dolomanov added a new response to »WBOX generated half of the necessary box«:

Yes, something wrong is going on...

Issue state: Unconfirmed → Confirmed.
Added 13 day(s) ago.

New issue »WBOX generated half of the necessary box« added by Ilia Guzei

WBOX malfunctions on a "grown" structure. For example, for urea it generates half of the box. Here is the offending file as saved from the CSD.

TITL UREAXX04
CELL 0.71073 5.576 5.576 4.686 90 90 90
ZERR 8 0.003 0.003 0.003 0 0 0
LATT -1
SYMM -y,x,-z
SYMM -x,-y,z
SYMM y,-x,-z
SYMM 1/2-x,1/2+y,-z
SYMM 1/2+y,1/2+x,z
SYMM 1/2+x,1/2-y,-z
SYMM 1/2-y,1/2-x,z
SFAC C H N O
UNIT 2 8 4 2
FVAR 1.00
C1 1 0.000000 0.500000 0.328400 0.250000 0.05000
O1 4 0.000000 0.500000 0.596600 0.250000 0.05000
N1 3 0.144800 0.644800 0.178700 0.500000 0.05000
H1 2 0.262000 0.762000 0.291000 0.500000 0.06000
H2 2 0.129000 0.629000 -0.042000 0.500000 0.06000
END

Added 13 day(s) ago.

Oleg Dolomanov added a new response to »FVAR«:

This mechanism just keeps the files clean, in particular if the users model disorder etc... Also FVAR used in more than in one expression will stay... I have to look if the FVAR's can get unmanaged

Added 14 day(s) ago.

Dr. John E Warren added a new response to »FVAR«:

This has come back. In this gas my "solvent" is gases such as Ar, Xe, Kr and sometimes I from an I2 complex.

As this are single atoms but which may be on a special position, I like to monitor them using a fvar. Especially if your tracking a series over multiple data collections. The use of -co or -o is nice but it is not brilliant when you are trying to plot the information as rather than copying a line out of the RES you have to look at each atom look at its occupancy, remember if it is on a special position, confirm this and then work out the actual occupancy. Rather than say 20.5 or 20.33333 etc and looking at FVAR 21.

I guess there is no way to override this behaviour in Olex2?

Added 14 day(s) ago.

Oleg Dolomanov added a new response to »Groups? Broken? Possibly?«:

OK, read it through, :) but cannot make the trunk crash, will try again...

Added 17 day(s) ago.

Oleg Dolomanov added a new response to »Groups? Broken? Possibly?«:

is the trunk behaves same way?

Added 17 day(s) ago.

Oleg Dolomanov added a new response to »Can't open a crs file«:

OK, Olex2 expects the Z to be an integer, whereas it has got the floating point in the given file. So for now you will have to put integer for Z, I will make it less picky in the next release.

Issue state: Unconfirmed → Confirmed.
Responsible manager: (UNASSIGNED) → Oleg.
Added 17 day(s) ago.

Ray added a new response to »Can't open a crs file«:

Here is a test *.crs file.

Added 17 day(s) ago.

Dr. John E Warren added a new response to »Can't open a crs file«:

Can you send an example crs file please?

Added 17 day(s) ago.

New issue »Can't open a crs file« added by Ray

I'm running Olex2 under Linux and I can't open any crs files provided by a Stoe IPDS2/2T (X-Area). I'm getting just this error:

@reap []
  Invalid integer format '1.00' at [sdl/smart/olx_istring.h(o_atoi_s):889]
Failed at [xlib/xfiles.cpp(LoadFromFile):52]
Failed at [xlib/xfiles.cpp(LoadFromFile):151]
Failed at [olex/xpprocs.cpp(macReap):4482]

Added 17 day(s) ago.

Dr. John E Warren added a new response to »No twinabs compatibility«:

Issue state: Resolved → Tested and confirmed closed.
Added 18 day(s) ago.

Dr. John E Warren added a new response to »No twinabs compatibility«:

Issue state: Unconfirmed → Resolved.
Responsible manager: (UNASSIGNED) → xrayman.
Added 18 day(s) ago.

Dr. John E Warren added a new response to »No twinabs compatibility«:

I actually added the compatibility to the source instead.

Added 18 day(s) ago.

Dr. John E Warren added a new response to »Absolute configuration determination thoughts«:

So does PLATON and you can use platon/Olex2 plugin

Added 18 day(s) ago.

Dr. John E Warren added a new response to »Groups? Broken? Possibly?«:

TRUNK
libc backtrace (1 frames, most recent call last):
  /lib64/libc.so.6 [0x32fe4332f0]

COULD this be related to the fact that on grow my molecule shares an atom with a symmetry generated version of itself which is NOT in the group?

Added 18 day(s) ago.

Dr. John E Warren added a new response to »Groups? Broken? Possibly?«:

 libc backtrace (49 frames, most recent call last):
  /home/xray/olexsvn/olexsvn [0x5f82d9]
  /lib64/libc.so.6(__libc_start_main+0xfd) [0x32fe41ea4d]
  /home/xray/olexsvn/olexsvn(main+0x12) [0xe6c032]
  /usr/lib64/libwx_baseu-2.8.so.0(wxEntry(int&, wchar_t**)+0x85) [0x3843897e15]
  /usr/lib64/libwx_gtk2u_core-2.8.so.0(wxAppBase::MainLoop()+0x4b) [0x33b866ac9b]
  /usr/lib64/libwx_gtk2u_core-2.8.so.0(wxEventLoop::Run()+0x48) [0x33b85e5fd8]
  /usr/lib64/libgtk-x11-2.0.so.0(gtk_main+0xa7) [0x394d3422b7]
  /lib64/libglib-2.0.so.0(g_main_loop_run+0x1a5) [0x32ffc3b535]
  /lib64/libglib-2.0.so.0 [0x32ffc3b0e8]
  /lib64/libglib-2.0.so.0(g_main_context_dispatch+0x22e) [0x32ffc3790e]
  /usr/lib64/libgdk-x11-2.0.so.0 [0x394da52a0c]
  /usr/lib64/libgtk-x11-2.0.so.0(gtk_main_do_event+0x203) [0x394d341d93]
  /usr/lib64/libgtk-x11-2.0.so.0(gtk_propagate_event+0x1f5) [0x394d340d65]
  /usr/lib64/libgtk-x11-2.0.so.0 [0x394d46739f]
  /lib64/libgobject-2.0.so.0(g_signal_emit+0x83) [0x3300422423]
  /lib64/libgobject-2.0.so.0(g_signal_emit_valist+0x67c) [0x3300421d6c]
  /lib64/libgobject-2.0.so.0 [0x330042080d]
  /lib64/libgobject-2.0.so.0(g_closure_invoke+0x15e) [0x330040b81e]
  /usr/lib64/libgtk-x11-2.0.so.0 [0x394d349b63]
  /usr/lib64/libgtk-x11-2.0.so.0 [0x394d480b6b]
  /usr/lib64/libgtk-x11-2.0.so.0(gtk_window_propagate_key_event+0x134) [0x394d47b724]
  /usr/lib64/libgtk-x11-2.0.so.0 [0x394d46739f]
  /lib64/libgobject-2.0.so.0(g_signal_emit+0x83) [0x3300422423]
  /lib64/libgobject-2.0.so.0(g_signal_emit_valist+0x67c) [0x3300421d6c]
  /lib64/libgobject-2.0.so.0 [0x3300420b43]
  /lib64/libgobject-2.0.so.0(g_closure_invoke+0x15e) [0x330040b81e]
  /usr/lib64/libgtk-x11-2.0.so.0 [0x394d349b63]
  /usr/lib64/libwx_gtk2u_core-2.8.so.0 [0x33b85fb109]
  /usr/lib64/libwx_baseu-2.8.so.0(wxEvtHandler::ProcessEvent(wxEvent&)+0xc7) [0x38438f3147]
  /usr/lib64/libwx_baseu-2.8.so.0(wxEventHashTable::HandleEvent(wxEvent&, wxEvtHandler*)+0xa4) [0x38438f3064]
  /usr/lib64/libwx_baseu-2.8.so.0(wxEvtHandler::ProcessEventIfMatches(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&)+0x50) [0x38438f20b0]
  /home/xray/olexsvn/olexsvn(TMainForm::OnChar(wxKeyEvent&)+0x341) [0xe20d51]
  /home/xray/olexsvn/olexsvn(glObj::TGlConsole::ProcessKey(int, short)+0x760) [0x794960]
  /home/xray/olexsvn/olexsvn(esdl::TActionQueue::Execute(esdl::IEObject const*, esdl::IEObject const*)+0xb7) [0x5fad87]
  /home/xray/olexsvn/olexsvn(TMainForm::Dispatch(int, short, esdl::IEObject const*, esdl::IEObject const*)+0x1aa3) [0xe268e3]
  /home/xray/olexsvn/olexsvn(TMainForm::ProcessMacro(esdl::TTSString<esdl::TWString, wchar_t> const&, esdl::TTSString<esdl::TWString, wchar_t> const&)+0x4b) [0xe2a03b]
  /home/xray/olexsvn/olexsvn(esdl::TEMacroLib::ProcessMacro(esdl::TTSString<esdl::TWString, wchar_t> const&, esdl::TMacroError&)+0x100a) [0x8efb9a]
  /home/xray/olexsvn/olexsvn(esdl::TMacro<TMainForm>::Run(esdl::TStrPObjList<esdl::TTSString<esdl::TWString, wchar_t>, esdl::IEObject*>&, esdl::TParamList const&, esdl::TMacroError&)+0x686) [0xe2e226]
  /home/xray/olexsvn/olexsvn(TMainForm::macGrow(esdl::TStrPObjList<esdl::TTSString<esdl::TWString, wchar_t>, esdl::IEObject*>&, esdl::TParamList const&, esdl::TMacroError&)+0x28e) [0xec146e]
  /home/xray/olexsvn/olexsvn(xlib::TLattice::GrowFragments(bool, esdl::TPtrList<xlib::TCAtom>*)+0x227) [0x8b60e7]
  /home/xray/olexsvn/olexsvn(xlib::TLattice::DoGrow(esdl::TPtrList<xlib::TSAtom> const&, bool, esdl::TPtrList<xlib::TCAtom>*)+0xeb0) [0x8b5cf0]
  /home/xray/olexsvn/olexsvn(xlib::TLattice::Disassemble(bool)+0x365) [0x8b2d95]
  /home/xray/olexsvn/olexsvn(esdl::TActionQueue::Exit(esdl::IEObject const*, esdl::IEObject const*)+0xc7) [0x5faca7]
  /home/xray/olexsvn/olexsvn(gxlib::TGXApp::Dispatch(int, short, esdl::IEObject const*, esdl::IEObject const*)+0x211) [0x824c61]
  /home/xray/olexsvn/olexsvn(gxlib::TGXApp::CreateObjects(bool, bool)+0x1838) [0x8238f8]
  /home/xray/olexsvn/olexsvn(gxlib::TGXApp::RestoreGroups()+0x1dd) [0x81a97d]
  /home/xray/olexsvn/olexsvn(gxlib::TGXApp::RestoreGroup(glObj::TGlGroup&, gxlib::TGXApp::GroupData const&)+0x2ba) [0x80534a]
  /home/xray/olexsvn/olexsvn(gxlib::TGXApp::SAtoms2XAtoms(esdl::TPtrList<xlib::TSAtom>&, esdl::TPtrList<gxlib::TXAtom>&)+0x2a) [0x804daa]
  /lib64/libc.so.6 [0x32fe4332f0]

Added 18 day(s) ago.