CCP4 Molecular Graphics - Symmetry Models

Introduction

It is often useful to display the symmetry equivalent molecules of a structure solved by crystallography. CCP4mg has two approaches to displaying symmetry related molecules
Using the crystal object This approach is more automated and is appropriate for crystallographic model building. One or more symmetry copies of the model are drawn to the display but only one copy of the model atomic data is stored in the program. If the model is changed (for example the structure is changed or the selection of displayed atoms is changed) then the changes will be reflected in all of the displayed copies.
or
Using the model tool Generate symmetry mates. This tool creates a copy of all the model atomic data, with only the atom coordinates changed (to the new symmetry related position). The original model and the symmetry copy can then be changed independently and any structure analysis or display tool can be applied to the two copies in a more flexible manner. This approach is useful for analysing or creating pictures of the crystal contact between symmetry related models.

Note that the cell and space group for the structure must be in the PDB file in the CRYST1 line. See the PDB Format Definition at wwPDB and the space group must match one of those defined in ccp4mg/ccp4_suite/lib/data/symop.lib. (Hint: the appropriate format for the space group name is the one in inverted commas at the end of the line.)

The Crystal Object

In CCP4mg a 'crystal' is an object which has the usual crystal symmetry parameters (cell dimensions, space group and symmetry transformations) and which can 'contain' one or more of the loaded models. The crystal object controls the display of symmetry related molecules. A crystal object is created automatically when an electron density map is loaded and can also be created if model coordinate data containing complete crystal parameters is loaded. The crystal object is shown at the top of the CCP4mg Display Table so after a map and a model have been loaded the Display Table will look like this

In addition to the entries in the table for the model and the map there is an entry for a Crystal object. The crystal object interface provides tools to control appearance of symmetry related copies of the model and to show crystal feature such as the unit cell edges. The three items of the crystal row in the Display Table are
Xtl Parameters The crystal symmetry parameters (space group and cell parameters) are, by default, taken from the map or MTZ file (it is usually more reliable!) but the source of crystal parameters can be selected from the menu listing all of the map, MTZ or coordinate files.
Crystal contents A menu lists all of the loaded models and these can be toggled on or off to be included in the crystal.
Display Style The options are

Continuous crystal This is the default mode which is most useful when performing crystallographic model building. Symmetry related copies of the model are generated automatically if they occupy a region of the crystal which is currently in view in the display. So as the user translates or rotates the display the appropriate symmetry models are generated to give the impression of a infinite continuous crystal. the next menu item "within radius" allows the user tp specify how large a radius should be searched for symmetry copies.
Contents one unit cell This shows all of the symmetry related copies which have some atoms within the volume of the unit cell edges (see below).
Crystal contacts This shows all of the symmetry related copies contacting the "central" copy.
Symmetry off No symmetry related copies are shown.
Colour carbon by symmetry This is on by default. The carbon atoms of the symmetry copies are coloured according to their symmetry operator.
Cell edges Toggles the display of the unit cell edges

To remove a crystal, click on the icon , and select Delete from the menu.

A crystal object can be created without loading a map. A coordinate file containing crystal symmetry parameters must already be loaded. From the File menu select Create object and crystal and select a coordinate file from which the crystal symmetry parameters will be read.

Symmetry can be turn on or off for a particular display object as shown in the picture below. By default "Apply symmetry" and "Draw central copy" are on for most objects. "Apply symmetry" is off by default for surfaces. Display object symmetry

Generate Symmetry Mates

This tool will create complete symmetry related copies of all of the structure data, retaining the same chain, residue and atom names but with the symmetry transformation applied to the atomic coordinates. Each symmetry copy can be handled independently - for example it can be addressed independently by selection and colouring tools. CCP4mg creates the symmetry copy in a new model. The model is the top level in the structure hierarchy of model, chain, residue and atom (see Coordinates IDs). The model level in the hierarchy is normally used for alternative NMR structures but CCP4mg is also using it for replicating symmetry mates.

This tool can be found on the model icon menu. The tool interface looks like this..

symmetry_gui

The top frame of the window interfaces to a tool to find the symmetry mates which are close to either the whole of the original model or some part of the model. To use this: select a cutoff distance and, if required, use the selection menu to choose a part of the model; then click on the Search for contacting symmetry mates button. By default, the search for neighbouring symmetry equivalent models is carried out over the range of 2 unit cells either side of the original model. If you suspect that this is not enough then there is an option to change the range.

The neighbouring symmetry mates are listed in a table and the model number for each symmetry mate is at the start of the line. The model data in the program now includes the symmetry mates - these will be displayed in a separate display object if the Show box is checked. The symmetry mates can also be shown in other display objects or used elsewhere in the program by selecting the model number or using the symid selection command.

The table shows the model number, the transformation and the short-hand symmetry id. You can add new symmetry mates by clicking the Add line button or add and remove lines using options on the icon menu . Changes are only applied after you have clicked the Apply button. Note that if you want to reapply the Search for contacting symmetry mates option that you will probably want to use the Clear option to remove existing symmetry mates first.

If you close and restart CCP4mg then the symmetry mates will be restored within the program but no change has been made to the coordinate file but if you wish to save the coordinates click on the model icon, and select File save/restore In an output PDB file the symmetry mates will be in separate MODEL section.

Symmetry id

The symmetry id is a short-hand representation of a symmetry transformation of the form n_xyz where n is the position of the symmetry operation in the syminfo.lib list of operations for the space group (it is therefore fairly arbitrary) and x,y and z are the translation in unit cell lengths with 5 added.

syminfo.lib

The symmetry information in CCP4mg is taken from the file:
ccp4mg/ccp4_suite/lib/data/syminfo.lib
This is (or should be) the same as the CCP4 program suite distribution of this file. If your data file has a space group label that is not defined in this file then CCP4mg will not create symmetry copies. You can fix problems by editing the syminfo.lib file particularly if you want to support an alternative space group name make a copy of the equivalent spacegroup entry, as shown here:

begin_spacegroup
number  8
basisop x,y,z
symbol ccp4 8
symbol Hall ' C -2y'
symbol xHM  'C 1 m 1'
symbol old  'C m'
symbol laue '-P 2y' '2/m'
symbol patt '-C 2y' '2/m'
symbol pgrp ' P -2y' 'm'
hklasu ccp4 'k>=0 and (l>0 or (l=0 and h>=0))'
mapasu ccp4 0<=x<-1; 0<=y<-1; 0<=z<-1
mapasu zero 0<=x<1; 0<=y<=1/4; 0<=z<1
mapasu nonz 0<=x<1; 0<=y<=1/4; 0<=z<1
cheshire 0<=x<=0; 0<=y<=1/2; 0<=z<=0
symop x,y,z
symop x,-y,z
cenop x,y,z
cenop x+1/2,y+1/2,z
end_spacegroup

and change the symbol old value to the spacegroup name that you have in your data.

Contents

Introduction

The Crystal Object

Generate Symmetry Mates

Symmetry id

syminfo.lib