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Cartesian coordinates from CIF file (Read 12944 times)
Gerrit-Jan Linker
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Cartesian coordinates from CIF file
17.05.08 at 08:20:41
 
Cartesian coordinates from CIF file
 
A CIF file, a Cristallographic Information File file (see for more details http://www.iucr.org/iucr-top/cif/) is a standard file format to interchange cristallographic data.
 
I want to convert the molecular structure defined in the file to cartesian coordinates so I can use it in Quantum Chemical calculations, in my MOLCAS calculations in this case. The information stored in the CIF file uses fractional coordinates and moreover the unit vectors are not orthonormal. This makes it difficult to convert the coordinates to cartesian xyz coordinates.
 
You can open a CIF file in a text editor to read its contents. The following section is an example where the unit vectors a,b and c are defined.
_cell_length_a                   7.1970(9)
_cell_length_b                   7.3430(6)
_cell_length_c                   11.948(1)
_cell_angle_alpha             93.454(7)
_cell_angle_beta                  75.158(6)
_cell_angle_gamma             97.405(7)

 
The cell lengths define the units along each axis. The coordinates of the atoms are given as fractions of these cell lengths.
 
The angle alpha is the angle between the vectors b and c
The angle beta is the angle between the vectors a and b
The angle gamma is the angle between the vectors a and b.
 
To convert the information in the CIF file to cartesian coordinates I used the Open Babel program (see for more information http://openbabel.org/wiki/Main_Page). The input format can be set to CIF and I used the Sybyl Mol2 format as output format since contains readable coordinates and it can also be read in by ChemOffice which I use to make ball-stick diagrams from the coordinates.
 
See also:
http://webmineral.com/crystal/Triclinic-Pedial.shtml
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« Last Edit: 21.05.08 at 20:58:15 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
Linker IT Software
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Gerrit-Jan Linker
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Posts: 75
enCIFer: CIF file viewer
Reply #1 - 16.07.09 at 08:39:53
 
enCIFer: CIF file viewer
 
The CIF file viewer enCIFer is available from  
http://www.ccdc.cam.ac.uk/free_services/encifer/
 
Load the cif file into the program. THen press the Visual tab.
 
To get a sense of the thermal atomic displacement (atomic positions are averaged) measured use the ellipic option in the styles menu by right clicking in the visual viewer.
 
To zoom in, hold the right mouse button and move the mouse pointer.
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« Last Edit: 05.09.09 at 20:52:53 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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