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conn
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n [r] atoms
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Sets the maximum number of bonds for the specified atoms to n and changes the default bond radius for the given atom type to r.
Examples:
- conn 5 $C sets the maximum number of bonds that all carbon atoms can have to 5.
- conn 1.3 $C changes the bonding radius for carbon atoms to 1.3 (the floating point is used to distinguish between n and r in this case!)
- conn 5 1.3 $C combines the two commands above
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compaq
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[-a] [-c] [-q]
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Moves all atoms or fragments of the asymmetric unit as close to each other as possible. If no options are provided, all fragments are assembled around the largest one.
- -a: assembles broken fragments
- -c: similar to the default behaviour, but considers atom-to-atom distances and will move all atoms to the closest possible position to the largest fragment in the structure.
- -q: moves the electron density peaks close to the atoms.
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addbond
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A1 A2 or atoms
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Adds a bond to the connectivity list for the specified atoms. This operation will also be successful if symmetry equivalent atoms are specified.
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delbond
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A1 A2 or Selected bond(s)
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Removes selected bonds from the connectivity list.
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sort
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[m] [l] [p] [h] atoms
[s] [h] [m] moiety
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The sorting of atoms in the atom list is very powerful, but also quite complex .
- -m: atomic weight
- -l: label, considering numbers
- -p: part, 0 is first followed by all positive parts in ascending order and then negative ones
- -h: to treat hydrogen atoms independent of the pivot atom.
Sorting of moieties
- -s: by size
- -h: by heaviest atom
- -m: by molecular weight
Usage:
sort [+atom_sort_type] TBA
sort [Atoms] [moiety [+moiety_sort_type] [moiety_atoms]] If just 'moiety' is provided - the atoms will be split into the moieties without sorting.
Examples:
- sort +m1 F2 F1 moiety +s will sort atoms by atomic mass and label, put F1 after F2 and form moieties sorted by size. Note that when sorting atoms, any subsequent sort type operates inside the groups created by the preceeding sort types.
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name
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[selection/atom names]
[-c]
[-s=]
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The command allows changing the atom names.
- -c: do not check if the generated names are unique
- -s: change the suffix only (no value removes the suffix, i.e. the part of label after the element symbol and numerical value)
Examples:
- name O1 O2: renames O1 to O2
- name 1: (some atoms selected) sequentially names the atoms in the order of the selection by adding 1,2, etc to the element symbol. Note that in this case if any generated name is not unique (and the -c option is not given), a random name will be generated
- name $q C: changes the element type of Q to C - all the electron density peaks will become carbons
- name sel -s=a: changes suffix of the selected atoms to 'a', replacing any existing suffix. Note that sel is a required keyword in this case (but may be removed in the future)
- name Q? C?: change type for all electron density peaks with single number label to carbon atoms preserving the number
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FixHL
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Updates H-atom labels according to the labels of the bearing atoms
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Olex2 will display the altered connectivity table in the case if structure is grown or packed
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