31 March 98
by N.Guex
Preferences
You can configure Swiss-PdbViewer in may ways, and save several different preferences files, which lets several users share the program with different settings. In any cases, a default preference file will be created and altered each time you quit the program. this file will contain the exact configuration present at the time you quit the program. If you want to alter your own preference file, you will have to explicitly save it.
It can be useful to make several
preference files, each of them containing for example
various rendering colours or bond sizes. Therefore, to alter
the display of a view, you will simply have to load a new
preference file. If you want to share a view that you like
with an other user, be sure to give him both the pdb file
and the preference file, otherwise, the appearance of the
molecule will depend on his own particular settings.
Note that preference files can be exchanged between PC and
Mac without problem.
- Modify last Prefs dialog
Redisplay the last preference dialog used to allow further modifications.
- Open
Replace the current settings (Default.prf) by those coming from an alternate file.
- Save
Saves the current settings in a file for future usage. Note that the current settings are always automatically saved in the "Default.prf" file when the user quits the program.
- General
This dialog mainly allows the user to alter the comportment of the program at startup and when a file is loaded.
- Loading Protein
You can use this dialog to alter the preferences so that a protein is automatically coloured by secondary structure, with a ribbon displayed instead of the traditionnal wireframe representation and superposed onto previously loaded proteins, with a structural alignment computed.
- Real Time Display
In order to insure a "smooth" handling of real-time molecule displacements, a number of options aimed to reduce the CPU load are provided. You can decide the degree of "realism" to allow when moving a molecule by deciding if you want Hydrogens to be drawn during the operation. The same is true for Sidechains. Besides, you can decide if you want to allow the molecule to be displayed in stereo during real-time operations.
To allow a finer control of the CPU load, you can modify the maximum number of lines to draw. If the number of lines to draw exceeds this threshold value, the program will first attempt to draw the molecule without stereo view, then without hydrogens, and eventually without sidechains. In order to reduce even more the CPU load, allow the program to draw only one group out of n by modifying the last dialog item. These options are especially useful on 68K Macs.
Note: the maximum number of lines that can be
drawn during real-time operations is deliberately limited to
15000 on Power Macs, 10000 on PC and 5000 on 68K Macs.
- EDM
This dialog lets you alter the colour of the electron density map, as well as the contouring sigma. The same map can be simultaneously contoured at two different sigmas with different colors. Two speed up rendering, you have the possibility to use a coarse contouring along one or several of the unit cell axis.
The unit cell axis are coloured in red for a, green for b and blue for c. You can easily mark where you are in the unit cell, as section are dotted, with a yellow mark every 10 sections.
Note that you can display the unit cell even when no electron density map is loaded. However, avoid to do it if you don't need it, as it will slow down the real time display.