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, 67 (Pt 4), 386-94

Presenting Your Structures: The CCP4mg Molecular-Graphics Software

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Presenting Your Structures: The CCP4mg Molecular-Graphics Software

S McNicholas et al. Acta Crystallogr D Biol Crystallogr.

Abstract

CCP4mg is a molecular-graphics program that is designed to give rapid access to both straightforward and complex static and dynamic representations of macromolecular structures. It has recently been updated with a new interface that provides more sophisticated atom-selection options and a wizard to facilitate the generation of complex scenes. These scenes may contain a mixture of coordinate-derived and abstract graphical objects, including text objects, arbitrary vectors, geometric objects and imported images, which can enhance a picture and eliminate the need for subsequent editing. Scene descriptions can be saved to file and transferred to other molecules. Here, the substantially enhanced version 2 of the program, with a new underlying GUI toolkit, is described. A built-in rendering module produces publication-quality images.

Figures

Figure 1
Figure 1
The CCP4mg main window and display table. Scene automatically created with Picture wizard style ‘ligand binding site: site and broken ribbons’ for PDB entry 1snf (Chan et al., 2004 ▶).
Figure 2
Figure 2
The Picture wizard. The selected style automatically created the scene shown in Fig. 1 ▶.
Figure 3
Figure 3
The electron-density styles possible in CCP4mg: (a) chickenwire, (b) chickenwire cylinders, (c) dots, (d) solid and (e) solid with transparency.
Figure 4
Figure 4
The text-display capabilities of CCP4mg. Three atoms are labelled with the default format: chain/residue number/atom name. The ligand has an annotation attached. All these rotate as the view is changed. In contrast, the ‘Legend’ is in a static user-defined screen position.
Figure 5
Figure 5
Structure and sequence alignment. Chain A of PDB entry 1eu5 (brown; González et al., 2001 ▶) superimposed on chain B of 2xce (pink; García-Nafría et al., 2010 ▶) using SSM. The nucleotide analogue dUpNpp bound to 2xce is drawn as cylinders. The sequences, aligned using MUSCLE, are displayed in the ‘Sequence viewer’ window coloured by conservation. The residues highlighted in the sequence viewer appear as stick representations in the graphics window. This figure also demonstrates the new single-window appearance of CCP4mg, with the Sequence viewer, Display Table and Clip and Fog widgets docked in the main window.
Figure 6
Figure 6
Assembly prediction by PISA. (a) The original model (PDB entry 3hhz; Green & Luo, 2009 ▶). (b) The dimer predicted by PISA.
Figure 7
Figure 7
The Movie editor dialogue. The above sequence rotates an expanded view of the molecule around the y axis for 2 s, takes 2 s to zoom into a close-up view of a ligand and then rocks for 2 s with the ligand at the screen centre.

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