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The Shelx file probably does not have the SFAC for Hydrogen so it would be good to add this in now. Manually edit the Shelx file and change:

SFAC      S   N   C
UNIT      1   6  10

SFAC      S   N   C   H
UNIT      1   6  10   9

You may like to copy this file into a new directory before running Crystals (or any other single crystal suite)

• Contact: david.watkin@chem.ox.ac.uk
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WinCRYSTALS 2000 (Crystals for Windows Single Crystal Suite) - David Watkin

• Contact: david.watkin@chem.ox.ac.uk
• Crystals Download
• Single Crystal Suite for PC.
• Original at http://www.xtl.ox.ac.uk/download.html
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Run Crystals and select the working directory using File, New Working Directory

Import the Shelx file using X-ray Data, Shelx file (INS or RES). As Crystals cannot interpret the Shelx symmetry operators to obtain a spacegroup symbol, when prompted input the spacegroup (P 21/A)

If Crystals has the number of atoms to search for in the Shelx file incorrect, input the correct number of atoms (in this case 17 instead of 8). If prompted, there are no Q peaks to rename, you don't want to look at the structure in cameron, and keep the present atom numbering.

Automatic Placement of Hydrogens but some Inaccurate Assignments

A note from David Watkin on this (in the context of Rietveld refinement before placing the hydrogens):

Date: Mon, 11 Sep 2000 13:46:27 +0100 (BST)
From: David Watkin [david.watkin@chemistry.oxford.ac.uk]
To: Lachlan Cranswick [L.M.D.Cranswick@dl.ac.uk]

I've looked at the cimetidine structure. Instead of trying to put H atoms
on just now, you would be better off using restraints to get the bond
lengths correct.  The C4-C17 bond on 1.7 A cannot be right - ie it is
wrong, so should be put right.  The C-Cmeth is short, so CRYSTALS thinks it
is SP2, as is the N-Cmeth.  A student last year wrote code to put H on N,
which will go into some future release, but guessing N hybridisatioon from
bond lengths is even more risky than C.

More information on "To restrain - or not to restrain"

Date: Wed, 13 Sep 2000 11:18:59 +0100 (BST)
From: David Watkin [david.watkin@chemistry.oxford.ac.uk]
To: Lachlan Cranswick [L.M.D.Cranswick@dl.ac.uk]

This is a deep philisophical problem, and draws in the
Bayesian/non-Bayesian people.  The non-Bayesians say that each experinent
should be treated as separate from any other, so you just refine as best
you can with the x-ray data you have.  The Baysians say that this is
daft.  If some other good experiment has given good values for something,
you should include this knowlwdge in the current process.  The trick is to
know what weight to give this external information.  A weight of zero makes
it a non-Baysian calculation.  A weight of infinity makes it a constrained
calculation. Other weights lead to restraints. 

Im a Bayesian myself.  If a bond length is weird, either its a fantastic
discovery, or its wrong.  If it's wrong - what's the point in publishing
it?  Put it right.  If the Rfactor goes up, then the data is rubbish and
needs improving.  If it stays about the same, then the data doesn't define the
parameter - but it may also fall showing that the trial model was poor.  If
one parameter is left at a poor value, others may take on incorrect values
to try to compensate - this is because the parameters are always correllated!

		Best wishes
					David

Automatic Placement of Hydrogens but some Inaccurate Assignments - cont'd

With the given caveates above: select Structure, Add Hydrogen and Crystals will now calculate the position of hydrogens off the carbon positions.

Note that depending on the accuracy of the Rietveld refinement to give decent bonds lengths and angles, Crystals may not get the correct Carbon type as it assumes high quality single crystal data is being used. For example it has not picked up the Methyl carbons correctly. One solution (most likely dodgy given the above comments by David Watkin) is to add the hydrogens to the offending carbons via scripts

Semi-Automatic Placement of Hydrogens

The above assignments were not adding the Methyl hydrogens correctly because the Rietveld refinement is not providing accurate enough atomic positions. As an exercise (in this case noting a bond length restrained Rietveld refinement may be a better option before proceeding) we will manually add the hydrogens to the two Methyl Carbons, then automatically add hydrogens to the rest of the carbon atoms where they are applicable. At present manual addition of hydrogens is done by the script interface but it can be expected this will also migrate to the GUI menu system in the near future.

If you have the hydrogens placed incorrectly already, select Structure, Remove Hydrogen

The options for hydrogen placement can be found with the computer based manual by selecting Help, Manual, Atomic and Structural Parameters; then select the webpage option of Hydrogen placing - \HYDROGENS

Via the bottom left script interface into Crystals (up arrow goes through previous commands), type:

\HYDROGENS and [ENTER]
H33 - then (using the mouse) graphically select the terminal C(15) carbon and two linking atoms - C(8) and C(13), and [ENTER]
H33 - then (using the mouse) graphically select the terminal C(16) carbon and two linking atoms - N(2) and C(11), and [ENTER]
END - to tell Crystals to perform the above instructions

The Sequence would look like the following on the script command line:

\HYDROGENS 
H33  C(15)  C(8)  C(13) 
H33  C(16)  N(2)  C(11) 
end

The will result in the C(15) and C(16) atoms having methyl hydrogens added to them.

Exporting the Structure from Crystals

An option on the latest Crystals is to select Publish, Platon which will output a Shelx *.RES file (after trying to spawn Platon).

If you do not want to spawn Platon, you could do the following from the script interface:

#FOREIGN PLATON
END

TITL THIS IS THE DEFAULT SETTING FOR THE TITL
CELL  0.71073 10.395 18.821  6.825  90.000 106.438  90.000
LATT  -1
SYMM  -X,Y+0.500,-Z
SFAC S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863 = 
           56.1720   0.8669   0.1100   0.1240    53.20   1.1100  32.0600
SFAC N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663 = 
            0.5826 -11.5290   0.0040   0.0030     1.96   0.7700  14.0070
SFAC C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650 = 
           51.6512   0.2156   0.0020   0.0020     1.15   0.7700  12.0110
SFAC H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408 = 
           57.7997   0.0030   0.0000   0.0000     0.06   0.3200   1.0080
UNIT    1.   6.  10.   9.

 
C10         3   0.14537   0.10713   0.50226   1.00000   0.15986
C17         3   0.23076   0.24856   0.05105   1.00000   0.15986
N3          2   0.12718   0.26397  -0.09963   1.00000   0.15986
N7          2   0.66623   0.01321   1.01608   1.00000   0.15986
S1          1  -0.01505   0.08600   0.28664   1.00000   0.15986
C9          3   0.62545   0.04915   0.86588   1.00000   0.15986
N6          2   0.59361   0.09115   0.70675   1.00000   0.15986
N5          2   0.21112   0.18304   0.14418   1.00000   0.15986
C8          3   0.02054   0.21236  -0.14908   1.00000   0.15986
C15         3  -0.10662   0.21903  -0.31759   1.00000   0.15986
N4          2   0.36836   0.05358   0.62421   1.00000   0.15986
C11         3   0.46025   0.09684   0.55470   1.00000   0.15986
C13         3   0.08636   0.16318   0.01014   1.00000   0.15986
N2          2   0.45503   0.12767   0.38842   1.00000   0.15986
C16         3   0.56797   0.15719   0.33445   1.00000   0.15986
C14         3   0.23440   0.03529   0.45789   1.00000   0.15986
C12         3   0.02512   0.08897   0.02411   1.00000   0.15986
H1          4  -0.10683   0.26514  -0.39046   1.00000   0.19183
H2          4  -0.18471   0.21758  -0.25939   1.00000   0.19183
H3          4  -0.11353   0.17883  -0.41585   1.00000   0.19183
H4          4   0.53697   0.17855   0.19481   1.00000   0.19183
H5          4   0.61082   0.19476   0.43547   1.00000   0.19183
H6          4   0.63465   0.11878   0.33554   1.00000   0.19183
H99         4   0.13071   0.10621   0.64086   1.00000   0.19183
H98         4   0.18687   0.15348   0.48198   1.00000   0.19183
H97         4   0.31339   0.27848   0.09619   1.00000   0.19183
H96         4   0.19503  -0.01093   0.48470   1.00000   0.19183
H95         4   0.24466   0.03504   0.31657   1.00000   0.19183
H94         4  -0.05884   0.08242  -0.09017   1.00000   0.19183
H93         4   0.09082   0.05086   0.01762   1.00000   0.19183