Chemical Crystallography Laboratory
University of Oxford

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Frequently Asked Questions

Chapter 8: Analysis

8.1: Find the angle between a plane of atoms and a bond

8.2: Calculate intermolecular distances

8.3: Find LIKELY H-BONDS with donors or acceptors other the O and N

8.4: How do I add hydrogen atoms to water molecules?

   \GEOMETRY
   ATOMS C(3) C(4) C(5) C(6) C(7) C(8)
   PLANE
   ATOMS C(1) O(2)
   LINE
   DIHEDRAL 1 AND 2
   END
 

This calculates the best plane of atoms C(3) through to C(8), and the line through the bond C(1) O(2). The dihedral command prints the angle between the vector normal to the best plane and the vector defined by the bond.
i.e. if the bond is at right angles to the ring, the angle will be zero, and if the bond is in the same plane as the ring, the angle will be 90.

Changing PLANE to LINE, or LINE to PLANE will allow you to find the angle between two planes or the angle between two lines!

    \dist
    select range=limits
    limit 2.0 4.0 2.0 4.0
    include N(6) O(8)
    end
 

This will give all the bond lengths and angles involving the specified atoms (so only bond lengths in this case!) that fall in the range 2.0 to 4.0 Angstroms. The first range 2.0->4.0 is for bonds, the second is for bond that form angles.
If you want su's too, then add this line before 'end':

     e.s.d yes
 

You can specify atom types instead of specific atoms, e.g. to look for only O-O contacts just use

     include O
 

The manual details other options for selecting atoms such as exclude, pivot etc.

 
   \dist
   out mon=all
   select range=limits
   limit 1.5 2.2 0.7 2.2
   pivot H
   bonded O N
   end
 

The 'pivot' atoms can only be at the centre of an angle or one end of a bond, and the 'bonded' can only be at the edges of an angle or the other end of the bond.
For other acceptors, add element to the BONDED directive (e.g. CL) in the above command and extend the bonding limits to something reasonable for a H--CL distance e.g. from 2.2 to about 3.7(?). It will then find all H--CL bonds and O-H--CL, or N-H--CL angles.
Becuase the distance command doesn't let you specify different limits for each side of an angle no distinction can be made between donors and acceptors, (i.e. you cannot get separate listings of O--H-N and N--H-O angles)

The following will work to find short O--O or O--N contacts in the range 2 - 3 Angstroms around a water atom O(6). Adjust the numbers on the LIMITS line to look at different ranges. Type this into the CRYSTALS command line (the small edit box below the text output), press return after each line.

     \DIST 
     OUTPUT MON=DIST 
     SELECT RANGE=LIMITS 
     LIMITS 2.0 3.0  0.0 0.0 
     PIVOT O(6)
     BONDED O N
     END
 

The PIVOT line specifies the single water atom (O(6)) at one end of the bond, while the BONDED line specifies that the other end of the bond must be a nitrogen or oxygen atom.
Once you have found a likely H-bond, say to O(21), you can place the H by typing in the following set of commands:

     \HYDROGEN
     DISTANCE 0.9
     HBOND O(6) O(21)
     END
 

i.e. O(6) is the donor and O(21) is the acceptor.


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