3D viewers

The additional integrated module, the ACD/3D Viewer, can visualize 2D structures as 3D models, after geometry optimization (see Section 2.12.3.1 and Figure 2-132, below). 

Molecule editors represent only two-dimensional chemical structures (thus also could be considered as 2D viewers), the third dimension is visualized by 3D viewers, mainly user-interactive. 

Some of the stand-alone programs mentioned above have an integrated modular 3D visualization application (e.g., ChemWindow —> SymApps, ChemSketch —> ACD/3D Viewer, ChemDraw —> Chem3D). These relatively simple viewers mostly generate the 3D geometries by force-field calculations. The basic visualization and manipulation features are also provided. Therefore, the molecular models can be visualized in various display styles, colors, shades, etc. and are scalable, movable and rotatable on the screen. 

ISlS/Draw has no genuine molecular visualization tool. The rotate tool changes only the 2D rotate tool into a 3D rotate tool which rotates 2D structures in three dimensions. In order to visualize chemical structures in different styles and perspectives, it is necessary to paste the drawing, e.g., to the ACD/3D Viewer. 

Figure 2-132. User-iinterface of the ACD/3D Viewer the bond angle between three marked atoms is displayed on the taskbar,...

Description 3D viewer molecular 3D viewer 2D editor. 3D viewer 3D viewer 3D viewer 3D viewer crystallo- 3D viewer ... 

For the 3D view of ISIS/Draw, ACD/3D Viewer Add-in can be installed. Retrieve ACD/3D Viewer for ISIS/Draw from http //www.acdlabs.com/downloar/ download.cgi and installed it as an Add-in according to instructions. To view 3D structure which is opened/sketched on the ISIS/Draw window, select ACD/3D Viewer tool from Object menu to open ACD/3D Viewer window and subsequent display of the 3D structure. The 3D structure can be optimized and can be saved only in, s3d format, which is not recognizable by other modeling packages. 

The basic evaluation includes the visual assessment of whole body images, using a 3D viewer, and the analysis of maximum intensity projection (MIP) images. Furthermore, a quantitative analysis of suspicious lesions and reference areas is recommended. 

The SRS 3D Viewer [28] is part of the SRS 3D server at the European Bioinformatics Institute (EBI) site (http //srs3d.ebi.ac.uk). Similar to Cn3D, SRS 3D is intuitive and easy to use. It enables the user to easily find all related structures, select one, and immediately see where the target sequence aligns onto the 3D structure (fig. 11.2B). Key differences between Cn3D and SRS 3D are that SRS 3D shows sequence features from the UniProt, InterPro, and PDB entries of the target sequence and enables users to easy map these features onto the structures (fig. 11.2C). SRS 3D also has a richer set of mouse and keyboard commands to help navigate and select parts of the sequence and structure. However, a drawback of the SRS 3D Viewer is that it can be difficult to install on some computers. SRS 3D is a commercial product but can be used freely via the Web to view any 3D structures in the PDB. 

ACD/3D Viewer Converts two-dimensional structures from ACD/ChemSketch into their three-dimensional counterparts and views, measures and handles them in virtual 3D, including setting up a rotational video http //www.acdlabs.com... 

These early studies are in agreement with our structural studies in determination of torsional angels and bond distances as calculated by ACD software 3D Viewer, Version 4.5 (Advanced Chemistry Development Inc. Toronto, Canada) and depicted in Scheme 2. 

Fig. 1 Structural comparison of aHL and VCH heptameis. Analysis was done using JSmol of 3D viewer, (a, b) are aHL (PDB No. 7AHL) and VCH (PDB No. 3044), respectively. Display style of these PFTs was selected as a cartoon style of display modes...

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