Toolbox Work

Toolbox Work

toolbox work-target

A collection of useful tools

  • Make all peaks Carbon
  • Move Atoms
  • Show/Hide Peaks
  • Expand Short Contacts
  • Peak Slider
  • Disorder Tools

shift-move-target

Move Atoms

  • Hold down SHIFT
  • Move atoms with left mouse button Split Atoms
  • Click on an atom to split it

Labels

You can select what you would like to see as labels in the molecule display. If a particular property is not applicable for a particular atom, there will be no label.

|help labels|To see all the command line options for the labels|

Toggle On/Off

This is to display or hide atom or Q-peak labels. It will switch other types of labelling off, but selecting it again will display atom name labels. [F3] does the same thing.

Atom Names

|labels -l| All atom names of non-hydrogen atoms will be displayed next to the atoms. |

Crystallographic Occupancy

|labels -o| This displays the crystallographic occupancy of any atoms which are not 100% occupied i.e. their occupancy is not 1. |

Chemical Occupancy

|labels -co| Displays the ‘chemical occupancy’ on the labels. Basically, the occupancy values for atoms that are located on symmetry elements are not shown. |

Parts

|labels -p| Displays PART numbers for any atoms not in PART 0. |

|labels -lo| If atoms are linked, the link code will be shown. (FVAR 21/-21 in ShelXL language) |

H Atom Labels

| labels -h -l | This will include the hydrogen atom labels along with the atom name and Q-peak labels |

Variables

| labels -v | Displays any atoms where the occupancy is linked to any variable |

AFIX Commands

| labels -a -h | This is useful to check the AFIX commands that are being applied to the structure |

Q-Peak Intensities

| labels -qi | Relative intensities of the Q-peaks will be displayed on the structure |

Residue Numbers

| labels -rn | Show the number of the residue an atom belongs to |

Residue Class

| labels -rc | Show the number of the residue class an atom belongs to |

Toolbar Model

This is a collection of three basic tools needed for model building.

Assign Atom Types

All atom types that are currently in your formula are represented as a small button.

Using the GUI

|$spy.MakeElementButtonsFromFormula(‘mode’)|All atoms present in the model are shown.|

You can click on one of these buttons and it will go into an atom type assignment mode for this particular atom type. Atoms you click subsequently will become that atom type. Alternatively, you can make a selection of atoms first, and then click the atom type symbol. The buttons will appear red if there are fewer atoms of that type in your model compared to the formula you have initially given. They turn green if the numbers do agree.

Using the Command Line

It is usually much more efficient to assign atom types using the keybard. Here are the three essential command you need to know:

|name sel C | Turns all selected atoms into carbon | |mode name C | Mode, where subsequently clicked atoms will turn into carbon atoms | |name \$Q C | Turns all Q-peaks into carbon atoms |

Geometrically Place Hydrogen Atoms

Pressing this button will cause Olex2 to place hydrogen atoms geometrically. If there is no selection of atoms, hydrogen atoms will be placed where possible. If there is a selection, they will only be added to the selected atoms.

|hadd| Adds hydrogen atoms to all selected atoms (or all, if none selected)| |hadd 137|Will use specifed AFIX if possible. (137 adds three hydrogen atoms to a methl group, for example.| |hadd -137|If the connectivity does not allow the addition of the specified AFIX atoms, it is still possible to place them in this way. Two atoms must be selected to denote a vector, with the atom to which hydrogen atoms are to be added selected first|

Toggle Isotropic/Anisotropic

With these buttons, you can make atoms either isotropic or anisotropic. If there is no selection this will apply to all atoms; if there is a selection, then this change will only apply to the selection.

|isot|All selected atoms will be refined isotropically| |anis|All selected atoms will be refined anisotropically (ellipsoids will result)|

Note: If the tickbox is ticked, then refinement will happen automatically after changing either isot, anis or hadd.

Quicktools

This is a selection of the tools needed for model building.

Affect atoms in the model or whether they are shown

|name \$Q C|$spy.MakeHoverButton(‘toolbar-QC’,‘name $Q C’)|This tool will change all visible electron density peaks to Carbon atoms, regardless of the peak height.|

|name \$Q H|$spy.MakeHoverButton(‘toolbar-QH’,‘name $Q H’)|All visible Q-peaks will be turned into Hydrogen atoms|

|clean|$spy.MakeHoverButton(‘toolbar-tidy’,‘clean’)|Tidy the Structure: Small and geometrically impossible peaks will be removed, all remaining peaks will be turned into Carbon.|

|kill \$H|$spy.MakeHoverButton(‘toolbar-killH’,‘kill $H’)|Deletes all selected Hydrogen atoms from your structure. If no hydrogen atoms are selected, all will be deleted. Undo with Ctr+Z.|

|showQ|$spy.MakeHoverButton(‘toolbar-Q’,‘showQ’)|CTRL+Q. Toggle between three states: Show electron density peaks, show them with bonds or hide them.|

|showH|$spy.MakeHoverButton(‘toolbar-H’,‘showH’)|CTRL+H. Toggle between three states: Show H atoms, show them with H-bonds or hide them. Hydrogen atoms remain in the model.|

|compaq>>compaq-a>>center|$spy.MakeHoverButton(‘toolbar-center’,‘compaq»compaq -a»center’)|Fragments will be assembled and the structure will be centered on the screen.|

##Affect the fomula of the structure |Z'|Set the value of Z' here. For a molecular structure this is typically the sum formula of the molecule. If there are two independent molecules on the screen, Z' must be set to 2. If the molecule needs to be grown, Z' will smaller than one (often 0.5).|

|fixunit|$spy.MakeHoverButton(‘toolbar-OK’,‘fixunit’)| Adjusts the sum formula to what is currently present in the model, taking the value of Z' into account.|

Part Links

This is a selection of quick-links regarding displaying of PARTS in your structure. The command-line equivalents are also very useful to know:

| showp 0 1 | Shows all atoms in no particular part and all atoms in PART 1 |

| showp 0 2 | Shows all atoms in no particular part and all atoms in PART 2 |

| showp 1 | Shows only the atoms PART 1 |

| showp | Show all parts|

| sel part 1 | Selects all atoms in PART 1 |

The use of the UP key is particularly useful in this context!

Split Group

The tools on this line will fully SPLIT the atom you click next into two atoms.

No Restraints

This will simply generate two atoms (at the focal points of the ellipsoids) and set the occupancies for each atom to 0.5. One of the atoms will be in PART 1, the other in PART 2. After the splitting has occured, you can move the newly ‘generated’ atoms to where you would like them to be (by holding the SHIFT key while moving them).

| mode split | Splits subsequently clicked atoms |

EADP

| mode split -r=EADP | This will split the atom as above, but will restrain the ADP values for both atoms to be the same. This is useful early on, and should probably be removed once the disorder model is nearly complete. You might want to apply the DELU restraint instead.|

ISOR

| mode split -r=ISOR | This will split the atom as above, and reply an ISOR restraint to each of the two atoms. |

SIMU

| mode split -r=SIMU | As above, but with a SIMU restraint. |

Disorder Tools

These are an extremely useful set of commands for dealing with crystallographic disorder.

Fit Group

This tool operates on a selection of atoms, which can consist of any number of atoms.

Fit or Split One Atom

Select one atom, then select whether you want to fit or split the atom. If you want to fit the atom, you can now move that atom with the left mouse to any position you like by pressing the SHIFT key; when you are finished, press the Esc key.

If you want to split the atom, you will now see two atoms, both of which you can move with the left mouse while holding the SHIFT key pressed. The occupancies of the two atoms are linked, and the atoms will now belong to different parts.

Fit or Split Two Atoms

Select two atoms, then select whether you want to fit or split the group. Split will generate a duplicate group, fit will not. While pressing the SHIFT key, you can move the selection as a group. While pressing the CTRL key, you can rotate the group around the midpoint between the two atoms.

Fit or Split Three or more Atoms

Select three or more atoms, then select whether you want to fit or split the group. Split will generate a duplicate group, fit will not.

While pressing the SHIFT key, you can move the entire group. You can now activate any bond around which you wish to rotate the group by right-clicking on it. While pressing the Ctrl key, you can rotate the group around this activated bond. When you are done, press the Esc key.

Split SAME

This is one of the most powerful tools in Olex2. If a grouping of atoms is disordered, and you can model one of the parts (no matter how badly), this tool is what you need. Simply select the entire grouping you wish to split, then press this button (or type mode fit -s same) and you can now generate a duplicate grouping. Everything will be constrained, so if this can be modelled, then the refinement will sort this out all by itself – sometimes a large number of refinement cycles is needed.

Split or move with SHIFT

This tool can also be used to move any atom (including Hydrogen atoms) to any position. Left click on the atom while pressing the SHIFT key - and you can move any atom where you would like it to be. Any constraints and restraints applied to that atom will still apply. When you are done, press the Esc key.

Note: If you click on an atom without holding down the SHIFT key, the atom will be split! So take great care with this tool!

Electron Density

The electron density viewer will calculate various electron density maps and allowsthe display of these in a variety of formats. Note: Close to zero, these maps become very messy (and slow to display). Olex2 therefore does not display these regions.

Available maps

diff

Will calculate the difference map.

fcalc

Will display the calculated electron density.

2Fo-Fc

Will calculate the map of 2Fobs-Fcalc.

Available Source

olex

Olex2 will calculate the structure factors.

fcf

The structure factors will be read from a ShelXL fcf.

|CalcFourier| Calculates the map according to the settings set in the map tool.|

Peak & Uiso Sliders

Electron Density Peak Slider

Electron Density Peak Slider Move the slider to the left to filter out strongest peaks first, or to the right to filter out weakest peaks first. You can then do things like name $Q C - and this will only apply to the currently visible peaks. The same goes for the Select and Delete buttons.

Uiso Select Slider

This tool allows the selection of atoms according to their Ueq values.

Slide to the RIGHT

This will select atoms where the Ueq value is LARGER than the value indicated by the slider.

|sel atoms where xatom.uiso > 0.06 xatom.type!='Q'| |

Slide to the LEFT

This will select atoms where the Ueq value is SMALLER than the value indicated by the slider.

| sel atoms where xatom.uiso > 0.08 | Selects all atoms where the Uiso value is larger than 0.08|

Growing

Olex2 shows the asymmetric unit by default. The tools combined here in three drop-down boxes are very powerful, and will allow you to ‘assemble’ your structure in exactly the way you want it to be. In Olex2 you can keep refining your structure without ‘destroying’ the assembly you have created.

Grow

Grow All

|grow|All ‘missing’ connected symmetry equivalent atoms will be generated.|

Shells

|grow -s|This will grow atoms shell-by-shell from the currently displayed image.|

Complete

|grow -w|This will generate all missing symmetry equivalent atoms of an already grown structure, independent of whether these are bound to the main fragment or not. In other words: all solvent molecules and counter-ion will be generated according to what is already shown.|

Asym. Unit

|fuse|Removes all symmetry equivalent atoms and displays the asymmetric unit.|

Complete shown growing bonds

|grow -b|If you are in a growing mode, then clickable growing bonds will be shown. All of these can be grown|

Mode Grow

|mode grow|Similar to grow, but now this command will be executed only after you click on an object. When you enter a growing mode, clickable ‘growing bonds’ will sprout from atoms where the kind of growing you have asked for is applicable.|

There are various modifiers for this command:

Short Contacts

|mode grow -s|Will show these growable ‘bonds’ to those atoms where ‘short interactions’ exist.|

Selection

|mode grow -r|Will show growable ‘bonds’ to other occurances of the currently selected atoms.|

###Van der Waals Radii |mode grow -v 2.0|Will show growable ‘bonds’ to other occurances of the currently selected atoms that are at least the indicated distance away from the selected atom.|

Move

|mode grow -a|When you click on growable bonds the symmetry equivalent atom will be moved to the new position. This is really useful when you are trying to assemble a meaningful asymmetric unit for extended structures (polymers).|

Shells

See above.

Assemble

This tool does not strictly belong to the ‘growing’ family of tools, but it is frequently used together with the growing tools. It allows you to re-arrange the asymmetric unit contents into a different configuration.

Broken Fragments

|compaq -a|Sometimes, your structure may become ‘broken’ - parts that should be bonded are shown as separate fragments. This tool will bring them back together.|

Atom-to-Atom

|compaq -c|Similar to the ‘Broken Fragments’ tool, but a different algorithm is used.|

Metal Last

|compaq -m|In this tool, metal ions are taken out of the equation at first (which is very useful when trying to assemble a ligand!) and then the metal ion is placed at the shortest possible distance.|

Q-Peaks

|compaq -q|This will move all electron density peaks as closely to existing atoms as possible.|

Finishing

Quick Sort

TBI - still!

Quick Images

TBI