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Scientific FAQs
 How do I obtain Mercury?
Mercury is distributed with the ConQuest search software as a part of the CSD System and also with DASH which is a program for
determining crystal structure from powder diffraction data. Mercury can also be downloaded free of
charge from the
Mercury Download page.
Note: Some of the advanced functionality in Mercury is only available only to registered Cambridge Structural Database (CSD) System subscribers.
Which file formats does Mercury support?
Mercury has its own file format (filename extension .mry) for reading and exporting files. In addition, Mercury can read crystal structures
from the following file types: cif, mol, mol2, pdb, res and sd format. It is also possible to export structures in either
cif, mol2, pdb or res format.
Can I save images displayed within Mercury as graphics files?
Yes, the current view can be saved as a graphical image in either Bitmap (*.bmp), Portable
Network Graphics (*.png) or jpeg (*.jpg or *.jpeg) file formats.
To save the current image, hit File in the top-level menu, Save As... in the next menu, then choose the required
format in the File Format dialogue box and hit OK. This opens the Save As dialogue box which allows you to specify the
name and location of the file to be created. The Save Image dialogue box then appears. This allows you to specify the image
size. Please note, sizes over 1500 by 1500 pixels require large amounts of memory.
Can I measure dihedral angles between planes?
Yes, planes can be used in distance measurements with other planes, atoms and centroids. Angles between planes can be measured.
Also, centroids can be used in distance, angle and torsion angle measurements.
Is there a way to change the colour and size of the H-bonds?
Yes, it is possible to change the colour and/or style of
specific non-bonded contacts. Right click on the relevant contact, then select either your chosen colour from
the Colour list in the pull down menu or by selecting your preferred representation from the Style menu.
Changes can also be applied to all contacts currently on display. To set the colour of contacts,
hit the top-level Display button followed by Colours in the resulting pull-down menu,
then Contacts... in the next menu. This will bring up the Colour Contacts dialogue box. Select By
expanded/hanging to display contacts according to the default colouring conventions, or Colour in
order to choose your own. If you select the latter, you should then click on the coloured panel to choose the colour you
want. The selected colour can be applied to All Contacts, Expanded Contacts or Hanging
Contacts as required.
To set the display style of all contacts currently on display, hit the top-level Display button followed by Styles in the
resulting pull-down menu, then Contacts... in the next menu. This will bring up the Contact Style dialogue box.
Select either Wireframe or Stick representation. The chosen display style can then be applied to
All Contacts, Expanded Contacts or Hanging Contacts as required.
Note: existing settings are not propagated
if, for example, the Packing tick box is activated.
Is there
any way to permanently alter the default atomic radii of atoms?
Mercury uses an internal set of atomic radii. A list of these radii can be found in the Mercury User Guide under the Van der Waals link (section 14).
It is not possible, in any of the formats that Mercury reads, to change the radii or tolerances used in determining structural connectivity.
Is it possible to view multiple structures simultaneously in the same window?
Yes, Mercury allows two or more structures to be displayed simultaneously. To display multiple crystal structures, switch
on the Multiple Structures tick box located under the list of structures on the right hand side of
the main Mercury window.
Note: The ability to display multiple crystal structures is only available to registered CSD System subscribers.
Having built up a network of molecules, can I delete one of them?
Yes - right click on any of the atoms or bonds in the molecule you want to delete, then select Delete this Molecule from the pop-up menu.
I am viewing a CSD entry / I have loaded a CIF/SHELX res/pdb file output from the CSD: why can't I view the displacement ellipsoids?
For ellipsoids to be displayed in Mercury, it is necessary for the relevant Uequiv and Uij
values to be present in the CIF or SHELX res file being read by Mercury. For PDB files ANISOU records are required
to be present in the file. Temperature factor parameters are not retained when a structure is input to the CSD,
thus it is not possible to view ellipsoids for entries stored in or output
from the CSD.
How can I view displacement ellipsoids for CSD entries?
ConQuest and Mercury contain DOIs for recent publications where available. Links are provided to the original article from these DOIs (in the case
of ConQuest via the CrossRef or IUCr buttons; in the case of Mercury via a hyperlink in the More
Info, Structure window under Literature Reference. For some recent publications CIFs are provided
on the publisher's website as supplementary data thus the original CIF (which may contain Uequiv and Uij data) may
be obtained in this way.
In addition, links are also provided from ConQuest to CCDC's
online request form via deposition number hyperlinks.
CIFs obtained using the online form may contain these data where provided
by the publishing author.
Can I output temperature factors from Mercury?
Currently, temperature factors (Uequiv and Uij for CIFs/res files, ANISOU records for PDB files) are written only to SHELX res and PDB files from Mercury.
How are the simulated powder diffraction patterns calculated?
The calculation used to simulate powder diffraction patterns in Mercury is fundamental thus no one
algorithm exists, rather a serious of steps need to be taken based on the theories of how X-rays interact with 3-D lattices. The publication
"Fundamentals of Crystallography" by C. Giacovazzo, H. L. Monaco, D.
Viterbo, F. Scordari, G. Gilli, G. Zanotti, M. Catti by Oxford
University Press and the IUCr (ISBN 0 19 855578 4) gives a good overview of the steps required to
generate a simulated powder diffraction pattern.
Can I use my existing style settings with Mercury 2.2?
For reasons outside of our control, Mercury 2.2 unfortunately cannot read
any settings saved by earlier versions of the program. This is most likely
to affect users who have used the Style Manager to edit Mercury's default
display styles, or to add new named styles of their own.
Before uninstalling the previous version of Mercury, users who want to
retain their customised styles should run the old Mercury, select Display,
Manage Styles..., and use the button to save any styles they wish
to keep. Then, after installing the new version of the program, open the
same dialog and use the Open... button to read in the saved .msd style
files.
I'm trying to use the Mercury-MOPAC link but keep on getting an error message: what does it mean?
If you receive an error of the type:
MOPAC job failed
Please check that you are running a correctly-installed copy of MOPAC 2007
or newer, and that the chosen Hamiltonian supports the elements in this
structure.
Please ensure the following:
- Is MOPAC installed in the default directory:
C:\Program Files\MOPAC\?
- Are you using MOPAC 2007 or newer? Note that versions of MOPAC older than 2007 are not supported.
- That the elements in the structure are supported by the chosen Hamiltonian, see http://openmopac.net/manual/.
- That you are not using the PM6 Hamiltonian to calculate ESP surfaces for compounds containing elements heavier than fluorine.
If you continue to experience problems please refer to the MOPAC user manual at the URL above.
I'm trying to pack a unit cell and Mercury is running very slowly/freezing.
Unfortunately this is a non-trivial problem we are working on resolving. It occurs when trying to pack
a crystal structure in a highly symmetrical spacegroup that contains large, highly symmetrical molecules on a special position or polymeric molecules.
The speed of packing of a single unit cell can be improved by opening the
Packing and Slicing dialogue via Calculate, Packing/Slicing, changing
the Include atoms radio button to ...that Fit. Once this setting has been changed,
activate the Pack tickbox. Mercury will display packing but only for the atoms
whose coordinates are at or within the boundaries of the packing range specified thus speeding up
the display of packing.
If you are packing more than one unit cell, we would recommend that you first
open Mercury (without loading your structure), open the Packing and Slicing
dialogue as above and change all appropriate settings (i.e. the Include atoms
setting should read ...that Fit,
activate the Pack tick box then change the a, b and c values to those
required). You can then read your structure in. Mercury will still take a reasonable amount of time to process
the settings and display the packing (also dependent on what your settings for a, b and c are)
however Mercury will eventually display the packing.
How do I reference Mercury?
Mercury References
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