Constraints/Restraints

Disorder Modelling: Constraints and Restraints

EXYZ

atom types (to add for the selected atom)
[-EADP]
[-lo]

Makes the selected site shared by atoms of several atom types.

  • -EADP: adds the equivalent ADPs command for all atoms sharing one site.
  • -lo: links the occupancy of the atoms sharing the site through a free variable.

 

EADP

atoms

Makes the ADP of the specified atoms equivalent.

SADI

atoms or bonds [esd=0.02]

 

For selected bonds or atom pairs SADI makes the distances specified by selecting bonds or atom pairs similar within the esd.

If only one atom is selected it is considered to belong to a regular molecule (like PF6) and adds similarity restraints for P-F and F-F distances.

For three selected atoms (A1,A2,A3) it creates similarity restraint for A1-A2 and A2-A3 distances.

DFIX

d atom pairs or pairwise selection in order [esd=0.02]

For selected bonds or atom pairs DFIX will generate length fixing restraint with the given esd.

If only one atom is selected, all outgoing bonds of that atom will be fixed to the given length with provided esd. For three selected atoms (A1,A2,A3) the A1-A2 and A2-A3 restraints will be generated.

DANG

d atom pairs or pairwise selection in order  [esd=0.04]

For selected bonds or atom pairs, distance restraints similar to dfix will be generated.

tria

d1 d2 angle [esd=0.02]

For given set of bond pairs sharing an atom or atom triplets generates two dfix commands and one dang command.

Example: tria 1 1 180 C1 C2 C3 will generate 'DFIX 1 0.02 C1 C2  C2 C3' and 'DANG 2 0.04 C1 C3' it will calculate the distance for dang from d1 d2 and the angle.

FLAT

[atoms][esd=0.1]

Restrains given fragment to be flat (can be used on the grown structure) within given esd.

CHIV

[atoms][val=0] [esd=0.1]

Restrains the chiral volume of the provided group to be val within given esd

SIMU

[d=1.7] [esd12=0.04] [esd13=0.08]

Restrains the ADPs of all 1,2 and 1,3 pairs within the given atoms to be similar with the given esd.

DELU

[esd12=0.01] [esd13=0.01]

'rigid bond' restraint

ISOR

[esd=0.1] [esd_terminal=0.2]

Restrains the ADP of the given atom(s) to be approximately isotropic

SAME

N

Splits the selected atoms into the N groups and applies the SAME restraint to them. Olex2 will manage the order of atoms within the ins file, however mixing rigid group constraints and the 'same' instructions might lead to an erroneous instruction file.

showp

[any]; space separated part number(s)

Shows only the parts requested: showp 0 1 will show parts 0 and 1, showp 0 just part 0. showp by itself will display all parts.

split

[-r={eadp, isor, simu}]

Splits selected atom(s) along the longest ADP axis into two groups and links their occupancy through a free variable.

  • -r: adds specific restraints/constraints (EADP, ISOR or SIMU) for the generated atoms

 

AFIX

shelx afix number{mn}
[-n]

If no are atoms provided and afix corresponds to a fitted group where n is 6 or 9 (such as 106 or 79), all the rings which satisfy the given afix will be automatically made rigid (this is useful in the case of many PPh3 fragments); alternatively a single ring atom can be selected to make that ring rigid. In other cases, depending on afix either 5,6 or 10 atoms will be expected. Special cases of afix 0, 1 and 2 can be used to remove afix, fix all parameters or leave just the coordinates refinable, all other afix instructions will consider the first atom as a pivot atom and the rest - dependent atom.

  • -n: consider N-atoms as parts of rings

 

part

[part=new_part] [atoms]
[-p=1]

Changes part number for given/selected atom;

  • -lo: links occupancies of the atoms through a +/-variable or linear equation (SUMP) depending on the -p[=1]
  • -p:   specifies how many parts to create. If -p=1, -lo is ignored and the given or new part is assigned to the provided atoms.

 

fvar

[value] [atoms]

This command links two or more atoms through a free variable.

  • If no atoms are given the current free variables are printed.
  • If no value is given but two atom names are give, the occupancies of those atoms are linked through a new free variable.
  • If a value of 0 is given, the occupancy of the specified atoms will be refined freely
  • if the value is not 0, the occupancy value of the specified atoms is set to the given value.

 

sump

[val=1] [esd=0.01]

Creates a new linear equation. If any of the selected atoms has refinable or fixed occupancy, a new variable is added with value 1/(number of given atoms), otherwise already used variable is used with weight of 1.0.

Example: If 3 atoms (A1, A2, A3) are selected this command will generate three free variables and insert the r2 1.0 var 3 instruction (equivalent to 1.0 = 1.0*occu(A1) + 1.0*occu(A2) + 1.0*occu(A3).

mode

split [-r={eadp, isor, simu}]

Splits subsequently clicked atoms into parts, or in combination with the Shift key can be used to drag an atom to change its position. While in the mode the newly generated atoms can be selected and moved as a group with Shift down or rotated when dragging the selection. The original and generated atoms will be placed into different parts.

  • -r: can be used to generate extra restraints or constraints for original and generated atoms (see also the 'split' command); values EADP, ISOR or SIMU are allowed

 
 

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