View

The sub-menu View is shown on the left. It allows:




Preferences

Set drawing preferences

Colours Preferences

Set colours for atomic species

Go to atom

Select an atom to center the plot.

Zoom in

Magnify the model

Zoom out

Un-magnify the model

Reset Scale

Reset the scale

Reset View

Reset rotations and scale

Clean labels

Remove all the labels from the plot

View Plane

Set the view plane

Sequence

Display the sequence (for protein only)

Polyhedra

Start the polyhedra visualization

Polyhedra Properties

Set the properties of polyhedra

Show Toolbar

Toolbar visible or hidden


Preferences


Some details about models and maps are reported. In the following image it is shown which properties of a model can be changed:



In the following image it is shown which properties of a map can be changed:



In order to get a better view of a model it is possible to tune the radius of the spheres representing the atoms and the radius of the cylinders representing the bonds. The atom colors can be modified.



This window provides some tools to set the properties of the polyhedra; it is possible to visualize or to hide some of them, it is possible to change the colors and  the transparency, to show or to hide the edges etc.


General drawing options can be set in the following window:


Other options are available through this window: grid, projection type and 3D view (using two-color glasses):



Using some (old) video cards some troubleshooting are possible: the model/map appears and disappears when it is moved/rotated. In this case the line smooth must be turned off



Preferences


Set the colors for atomic species:



and the colors for chains,  secondary structures and residues (when working with proteins):



Go to atom


Using this interface it is possible to select an atom to center the model / map



or, if the structure is a protein:




View Plane


Set the preferred view plane..


Sequence


If the structure is a protein the information about the sequence is accessible. Different colors refers to different secondary structure elements (See Colours Table). By clicking on a residue the map/model is centered on it.




Copyright © 2011, Institute of Crystallography - Cnr Italy

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