other viewing functions

Introduction:
Under the View pulldown, there are some additional viewing functions like ball or one-letter representation for amino acid, turnning the topology upside down, etc.

Description:
Choose View/Zoom In (or Control+i) and View/Zoom Out (or Control+o) to change the size of the topology displayed on the VHMPT window. This can also be done by holding the 3rd mouse key (the rightmost one), then slowly move downward or upward to zoom the topology in and out, respectively. Users can also drag the middle mouse key (or the right and bottom scrollbars) to move the viewing window around the topology. (Clicking the arrows on two sides of the window scrollbars can fine tune the position of the viewing window.)

Choose View/Appearance/White Letter Code, View/Appearance/Color Letter Code, and View/Appearance/Color ball to change the ways the amino acids of the protein are shown. Note that different colors represent a different conservation score of the amino acids.They vary from blue-> white -> red which correspond to the conservation score of 0 -> 0.5 -> 1. Note that some information about the amino acid is given in the message window (below the Menu bar). The information shown in the message window includes the .msf file name, the .helixseq file name, the residue number of the current amino acid pointed at by the cursor and its type, the consensus amino acid of the aligned position on which the pointed amino acid is located, the conservation score of that position, and all the amino acids aligned in that position. Fig. 23 shows the result of selecting View/Appearance/Color Letter Code.

Fig. 22

If an upside down view of the topology is desired, choose View/Upside Down. Fig.24 shows the result of such an operation.

Fig. 23

Note that when the amino acid in the topology is represented in one-letter code, you can also use View/LetterCode Font/Size to change the letter code's font (or size, weight, etc).