Technical FAQs
 Which platforms are supported?
Mercury 3.0 is supported on the following platforms and operating
systems:
- Windows - Intel compatible Windows XP/Vista/7
- Linux - Intel compatible, 32 bit:
- RedHat Enterprise 4, 5, 6
- SuSE Linux Enterprise [Desktop|Server] 10, 11
- Debian 4, 5, 6
Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.
- Mac Intel compatible:
- Mac OS X 10.5, 10.6, 10.7
Mercury has been tested when installed natively on these platforms.
Use
with emulators, including virtual machines, has not been tested & is not supported.
If you choose to use a version other than those listed above we cannot
guarantee that Mercury will work correctly, although we will attempt to
assist you with any problems you may encounter.
Mercury will not read my CIF input file. What am I doing wrong?
Mercury expects certain information to be present within an input file - if certain key data are not present, then
Mercury may fail to read in the file.
In the case of CIFs, the spacegroup must be specified with at least one of the following must be supplied:
_symmetry_space_group_name_h-m
_symmetry_equiv_pos_as_xyz
_symmetry_Int_Tables_number
Additionally, all of the following CIF data names are required by Mercury:
_cell_length_a
_cell_length_b
_cell_length_c
_cell_angle_alpha
_cell_angle_beta
_cell_angle_gamma
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
We would also recommend the use of the CCDC's free CIF editor enCIFer to help correct CIFs for input into
Mercury. It can be downloaded here.
Why do I get an error from WebLab Viewer or ChemWeb when I try to view the Mercury Help files?
WebLab viewer and ChemWeb both use the standard Windows file extension ".chm" as one of it's own file formats, even though this should
be a standard Microsoft extension - hence WebLab viewer is mistakenly called to open this help file and an error occurs.
The solution is to delete the file Mercury.chm located in the doc directory of your Mercury installation - Mercury
will then try to open the Mercury.html help file instead.
How do I get Mercury
to recognise that I have a version of the CSD database installed?
If Mercury does not automatically open the CSD database when started, then it may be having difficulty locating the
appropriate database files. In such a case, Mercury will check the environment variable CCDC_TOOLKIT_ASER_DATABASE. If
this points to an ASER database, the database will be opened.
For example, on Windows:
SET CCDC_TOOLKIT_ASER_DATABASE=X:\cdromV525\csd\as525be
and on Unix (C shell):
setenv CCDC_TOOLKIT_ASER_DATABASE /home/cdrom/csd/as525be
Why do I have a problem displaying labels on Linux?
The latest version of Mercury tries to use the native OpenGL libraries for
your Linux distribution. However if you are experiencing any problems with
Mercury's display this is most likely because the OpenGL libraries on your
system cannot support all the functions that Mercury uses. In this case you
can switch back to using the libraries which are distributed with Mercury by
starting mercury from the command line with the flag "-mesa".
Whenever I try to start Mercury on my linux system I get an error message about "GCC_3.3 not found"
If you get the following error message
path-to-mercury/c_linux/lib/GCC/libgcc_s.so.1: version `GCC_3.3' not found (required by /usr/lib/libstdc++.so.6)
when starting Mercury, then this signifies that your Mercury installation is getting confused with which gcc libraries it should be using. The simplest way to
remedy this is to force the use of your system libraries by performing the following steps:
cd path-to-mercury/c_linux/lib/GCC/
mv libgcc_s.so.1 libgcc_s.so.1.old
Where path-to-mercury should be replaced to the path to your Mercury installation (e.g. /usr/local/Mercury_1.4 ).
In ConQuest on Mac OS X, the buttons on the Build Queries tab launch minimised windows: what can I do about this?
Presumably you are using the window manager twm? If you are using twm, you should:
cp /usr/X11R6/etc/twm/system.twmrc $HOME/.twmrc
and add a line RandomPlacement, save the file, and restart twm.
A more integrated window manager is shipped with Mac OS X called quartz-wm. To use quartz-wm:
cp /usr/X11R6/etc/xinit/xinitrc $HOME/.xinitrc
comment out twm &, add quartz-wm &, save the file and restart the XServer.
On Mac OS X I am
unable to open the teaching subset database
The Mac OSX distribution of Mercury 2.2 lacks the teaching subset
database files. To view the teaching subset database in the Mac OSX
version of Mercury 2.2, please download the subset database files to your computer
and then unpack the contents. The subset database can then be loaded
into Mercury via the File->Open menu.
I get an error trying to install on Windows "Installation ended prematurely because of an error"
Go to Start -> Run and enter "regsvr32 vbscript" (without the quotes),
then click OK. You should get a dialog saying "DllRegisterServer in vbscript suceeded".
Mercury should now install correctly
On linux, Mercury has a
transparent window and/or shows strange artefacts
This can be caused by having desktop effects enabled on your linux
system. To determine if this is the cause, please disable desktop
effects and see if Mercury launches properly.
If it does, then you can eliminate the problem even with desktop
effects enabled by editing the script run_application.sh and
add the line
XLIB_SKIP_ARGB_VISUALS=1; export XLIB_SKIP_ARGB_VISUALS
somewhere before the end.
On linux, Mercury displays no or
strangely formatted text in the graphical user interface
This problem is due to a default font that the graphical user
interface uses not being installed on your system.
The solution is to use a '-font' argument when starting, eg:
mercury -font -adobe-courier-bold-r-normal-*-12-120-75-75-m-70-iso8859-4
However, that font may not be on your system. All the fonts on your
system can be listed using the command 'xlsfonts', or you can use
'xfontsel' to build up the font string piece by piece, to find something
pleasing to your eye.
Ultimately, the font string may be added to the end of the last line of
the run_application.sh script that launches Mercury, to make the change
permanent.
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