Welcome to the SHADE3 server

Simple Hydrogen Anisotropic Displacement Estimator

(The server has moved to a new machine! see below.)

(New: Allows ab-initio (Crystal09) or experimentally derived internal motion.
All features of SHADE2 available.) see below

Please upload a cif file containing the molecule for
which anisotropic hydrogen atoms should be estimated.

Help

First of all, please notice that this server is in development. Your comments and bug reports will be greatly appreciated and we will try to respond quickly with an updated version. We recommend that you critically inspect the resulting ADPs using a visualization program, e.g. Ortep, Platon, Mercury or Peanut. The procedure and underlying program has been thoroughly tested, but the server setup (including the use of cif files) may contain bugs.

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 Å² in the bond direction and 0.02 Å² 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].

About the program

The shade server is written in python, and uses the PyCifRW parser to read and write cif files. The rigid body analysis is performed by the THMA11 program.
The program is released under the GNU general public license.
Author: Anders Østergaard Madsen.

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 SHADE3.

SHADE has been updated (may 2014)! A publication describing the details and comparisons with neutron-diffraction data and other methods of estimating H ADPs is soon available. There are two major changes to the server:

1: Combine with Crystal09 periodic calculations:
It is now possible to combine the results of periodic ab-initio calculations with SHADE, to get even better estimates of H motion. In principle any code that can provide calculated normal mode frequencies and coordinates, or even better estimated mean square displacements corresponding to internal molecular motion can be used. We provide a setup for using the Crystal09 program. The routine is as follows:
1. Use the Crystal09 program to calculate normal mode coordinates and frequencies at the gamma-point. We provide help to create the necessary input file, based on your CIF file. Follow this link Cif2Crystal
2. Run the Crystal09 or Crystal14 program on the input file. Depending on the size of your system and the available computational environment, this may take several days of number-crunching.
3. Use the Crystal09 output to modify your CIF to internal mean square displacements for all the atoms in your structure. We provide the tool to help you. Follow this link: Crystal2MSD
4. Submit the new CIF to the SHADE3 server.

Example input
Here are some example input files for xylitol:

Structure from Neutron experiment. This file should be submitted to cif2crystal to make Crystal09 input.
Output from Crystal09 based on the neutron structure . Can be used to create a SHADE3 compatible cif file on the Crystal2MSD server.
Example SHADE3 input based on the neutron structure.
Example SHADE3 input based on the X-ray structure, including scaled neutron ADPs (for comparison with the estimated values).

2: Include information from spectroscopic measurements:
If you have complementary data on your system from e.g. spectroscopic data, it can be used to assess the internal motion of the hydrogen atoms. A special cif-entry must be used for this purpose. If H4 is known from spectroscopy to have stretch, in-plane and out-of-plane vibrations of 3000, 2000 and 1000 cm-1 respectively, the input is as follows:

loop_
_atom_site_internal_mode_label
_atom_site_msd_bond_direction
_atom_site_msd_in_plane
_atom_site_msd_out_of_plane
H4 3000 2000 1000

Likewise, input in the form of mean square displacements can also be used, i.e. if H4 has got mean square displacements in the stretch, in-plane and out-of-plane directions of 0.005, 0.01 and 0.02 Å^2, the input should be:

loop_
_atom_site_internal_mode_label
_atom_site_msd_bond_direction
_atom_site_msd_in_plane
_atom_site_msd_out_of_plane
H4 0.005 0.01 0.02

Notice that the same construction is used for the displacements supplied as either frequencies or mean square displacements. When the numbers are smaller than one, they are considered to be mean square displacements, or otherwise frequencies.
Please remember, that all restrictions from SHADE2 are still present. For example, if you have a structure with more than one molecule in the assymmetric unit, before submitting cif file to SHADE3 you need to divide your cif file into seperate files with different molecules.

Information about SHADE2.

SHADE has been updated in several ways. A publication describing the details and comparisons with neutron-diffraction data and other methods of estimating H ADPs has been published:

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.

The SHADE library of internal displacements has been altered to give an overall better fit with ADPs from neutron diffraction experiments.
Furthermore, it is now possible to perform a segmented rigid body approach with shade. This approach uses the 'attached rigid groups' method implemented in the THMA11 program (here is the manual). To instruct SHADE to use attached rigid groups, a non-standard cif-loop should be put in the cif-file.

--- example cif entry ---
loop_
_segmented_tls_axis_defining_atoms
_segmented_tls_atoms_in_segment
'C26 C25' 'N3 N4 N5 N6 HN6'
'C6 C5' 'C7 C8 C9 S1 C10 O3 O2 C11 H9 H8 H11A H11B H11C'
'C20 C17' 'C21 C22 C23 C24 C26 C25 N3 N4 N5 N6 HN6 H24 H23 H22 H21'
'C14 C13' 'C19 C18 C15 C16 C17 H16 H15 H19 H18'
'N2 C5 C2 N2 N2' 'C12 C2 N1 C1 C4 C3 O1 C27 C28 C29 C30 C13 H12A H12B H12C H30B H30A H30C H29A H29B H28A H28B H27A H27B'
--- end of cif input ---

The input is closely tied to the THMA input. THMA allows at most
7 attached rigid groups, and this limitation of-course persists.

The _segmented_tls_axis_defining_atoms entry should contain
either two or five atom names in a list enclosed by quotation marks,
each atom name separated by white space. If two atoms are present,
they define the libration axis (similar to THMA entries LBAT1 and LBAT2). If five atoms
are present, this signals another way of constructing the libration
axis. This corresponds to a negative NAFA entry in THMA. The five
atoms then corresponds to LBAT1, LBAT2, LBAT3, LBAT4 and LBAT5, as
defined in the THMA manual.

The _segmented_tls_atoms_in_segment entry should be a quotation- mark-enclosed white-space delimited list of atom names corresponding to the atoms affected by the libration of the segment,
including H-atoms, though they are not part of the TLS analysis.

This could probably be explained better, so don't hesitate to ask if
it is unclear!