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Last
modified
31 March 98
by N.Guex
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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.
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