Bug reports, requests for improvements and all other sorts of comments are greatly appreciated and should be sent to Anders Ø. Madsen

Mail list

If you wish to get a notice about updates of the software you can send a mail to Anders Østergaard Madsen.

Requirements / Limitations

• The cif file should contain a description of one molecule in a crystal. The ADPs of the non-hydrogen atoms will be analysed using the THMA11 program (Trueblood and Schomaker, 1968) as a rigid body using the TLS formalism. This rigid body motion will be imposed on the hydrogen atoms along with a contribution from internal motion. In the present implementation this internal motion is taken from a database of displacements derived from accurate neutron diffraction structures. If a H atom does not belong to a fragment present in the database, we use a mean square displacement of 0.005 Ų in the bond direction and 0.02 Ų in the directions perpendicular to the bond.

• Atoms will be recognized by the THMA11 program on the basis of their name - so all H atom names should start with an H, e.g. "H5", "HO1", all carbon atoms with a C, and so on.
• If your crystal contains more than one molecular entity, you have to split the cif file into several files containing each entity.
• Only rigid fragments with at least 4 non-hydrogen atoms can be analyzed. The rigid body analysis is a procedure where the rigid-body translations (T) and librations (L) and their correlation (the S matrix) are fitted against the ADPs of the non-hydrogen atoms. There must be a sufficient amount of data for the fitting procedure. Each non-hydrogen atom have 6 anisotropic displacement parameters. If the fragments are smaller than 4 non-hydrogen atoms, the server will revert to a 'riding motion' procedure, where the overall TLS motion is replaced by the motion of the atom that the H atom is bound to.
• At present, the program does not take internal molecular symmetry into account. Thus, a full ADP matrix should be included for each and every atom in the molecule.
• Structures containing more than 280 atoms can not be analyzed, because of a limitation in the THMA11 program.

Citation(s)

Please cite the following paper
when you use SHADE for your research

SHADE web server for estimation of hydrogen anisotropic displacement parameters.
Anders Østergaard Madsen. J. Appl. Cryst. 39, 757---758 [reprint].

Related papers

• A simple approach to estimate isotropic displacement parameters for hydrogen atoms. Anders Ø. Madsen and Anna Agnieszka Hoser.
  Acta Crystallographica. Section A: Foundations of Crystallography (2015). 71, 2, 169-174.
  DOI: 10.1107/S2053273314025133

• SHADE3 server : a streamlined approach to estimate H-atom anisotropic displacement parameters using periodic ab initio calculations or experimental information. Anders Ø. Madsen and Anna Agnieszka Hoser.
  Journal of Applied Crystallography (2014). 47, 6, 2100-2104.
  DOI: 10.1107/S1600576714022973

• Estimated H-atom anisotropic displacement parameters: a comparison between different methods and with neutron diffraction results [ reprint ]. Parthapratim Munshi, Anders Ø. Madsen, Mark A. Spackman, Sine Larsen and Riccardo Destro. Acta Cryst. (2008). A64, 465-475.

• A neutron diffraction study of Xylitol: derivation of mean square internal vibrations for H atoms from a rigid body description. [reprint] Anders Østergaard Madsen, Sax Mason and Sine Larsen. Acta Cryst. (2003) Section B59, 653-663.

• The modeling of hydrogen atoms in charge density analysis [reprint]. Anders Østergaard Madsen, Henning Osholm Sørensen, Robert F. Stewart, Claus Flensburg and Sine Larsen. Acta Cryst. (2004) Section A60, 550-561.

• Charge density study of naphthalene based on X-ray diffraction data at four different temperatures and theoretical calculations. Jette Oddershede and Sine Larsen. J. Phys. Chem. A 2004, 108, 1057-1063.

About the program

Citations and links

• THMA11
  On the Rigid-Body Motion of Molecules in Crystals. Schomaker, Verner and Trueblood, K. N.. Acta Cryst. (1968) Section B24, 63-76.

  Correlation of internal torsional motion with overall molecular motion in crystals. Schomaker, Verner and Trueblood, Kenneth N. Acta Cryst. (1998) Section B54, 507-514.

• PyCifRW homepage

• PEANUT.
  Peanut: Computer graphics program to represent atomic displacement parameters. Journal of Molecular Graphics (1990), 8, 214-220.

• Platon homepage

• Mercury homepage
  

Changes

• 15 01 2017
  The server has moved to a new machine. Some security features have been enabled. This should not change functionality or performance.
  

• 3 09 2011
  New feature: if you submit ADPs without associated standard uncertainties, you can use the following option to use unit weights in the TLS analysis: Input the following entry in the cif file:
  _shade_thma_unit_weights yes
  

  Now SHADE gives input in the correct format for the MoPro program.

• 13 08 2011
  Version 2.1: More liberal atom labeling: Parentheses and longer atom names are allowed.This feature is accomplished via a new internal labeling for the thma11 program. This labeling is output in the cif files, in order to ease the interpretation of the thma input and output.

• 20 06 2008
  Reprint of new publication added to homepage.

• 15 04 2008
  SHADE2 made available.

• 16 08 2007
  The thma11 program, and thus SHADE, has been dimensioned to analyze up to 280 atoms.
  

• 13 08 2007
  Fixed a bug related to the use of _atom_site_U_iso_or_equiv values of zero in the submitted cif file. Thanks to Parthapratim Munshi for reporting this bug.

• 05 07 2006

  Upgraded to PyCifRW 3.0. This fixes the incompatibility problem with PLATON. Thus, PLATON is now able to read the CIF files produced by SHADE.
  Bug related to metal-organic structures have been fixed.
  I discovered that analysis of structures of more than 150 atoms is presently not possible due to limitations in the THMA11 program.

Information about SHADE2.