Scene parameters:


These parameters specify the parameters of the scene. The default values will ensure that the protein is at the centre of the image. You can however specify precisely the orientation of the protein, by filling the fields "Centre on" and "Focus on". This will specify a line that goes from the point specified as the centre to the eye of the user, passing through the point defined as the focus.Additional rotations can be applied (see the section Advanced parameters).
You could find exemple of the use of theses options in the focus picture tutorial.


Centre on: This specifies a coordinate that will be placed at the center of the image. It can be on the form of the specification of a residue name, or atom name, or on the form of an explicit coordinate. By default, the centre of mass is used (Center on "auto"). The specification of a residue or atom must be on the form: C.RNI.A, where C is a chain label (1 letter,[A-Z,a-z] " " blank character is accepted), R, a residue name (3letter code, 1 letter code possible for the 20 classical amino-acids), N the PDB file residue number (Important: some PDB files do not start at residue 1). Here, we do you the numbers of the PDB file. The sequence visualization facility accessible from the form offers a mean to check residue numbers), I is the PDB insertion code (if any), A is an atom name (valid in the residue specified). For example, "A.ARG241B.CB" denotes the carbon beta of the arginine 241B (insertion code B) of the chain A. A.R241B.CB would also be valid. For unique no-name chain protein, this kind of command : " .CYS3.SG" should be used.
Alternatively, you could edit the PDB file, pick up the coordinates and specify for instance: 59.59 25.911 7.571 or 59.592,25.911,7.571 (use a dot in numbers and not commas, since commas will be removed).

Focus on : specify a residue, atom, or coordinate to place on a line that goes from the Centre (define by center on) towards the eye of the user (Z axis). By default, the PDB file Z axis is used (Focus on "auto"). Advanced parameters allow to specify translation on X, Y and Z axis to adjust the view.

View Angle : specify the field of view angle of the camera for the picture generation. The value should be positive. Reasonable values are within the range 10..110. The "auto" value will trigger calculation for a reasonable value.