Dear Swiss-PdbViewer users,


We are glad to announce the availibility of version 3.7b1
This is a stable beta, wich corrects several glitches of
the version 3.6 and also introduces some new features
among which the first version of the scripting language.

Also, note that the IP address for spdbv direct server
has changed. The new address is now
www.gwer.ch  (213.39.71.210) You need to modify your
network preferences.

Have fun,
Nicolas, Torsten & Alexander.

----------------------------------------------------------------------
Comments about this release.
----------------------------

Mac, PC, SGI, Linux
===================

-The first version of the scripting language is now available
 Examples are provided in the distribution and located in
 the scripts directory. There is also a Manual with the list
 of supported commands. This will evolve in the future
 The scripting language will be quite familiar for persons
 who know C or perl. The scripting language supports
 variables, conditionnal branching, loops, arrays and
 file access. The scripts can be stopped at specific points
 to let users interact with the graphical interface before
 resuming operation. You can use scripts and subroutines
 to add commands to the interface.

-It is now possible to specify the spdbv server by name
 (www.gwer.ch) or by IP (213.39.71.210).

-Some items of the select menu have been reorganized (nothing
 has been moved to other menus, this is just a regroupment
 of items that are similar).

-The Display window preferences (previously accessed from
 the leftmost icon of the toolbar is now accessed from
 the "Display..." item of the Prefs menu. Some items
 concerning the stereo preferences have been removed as
 they were also present in the Stereo Preferences.

-The leftmost icon of the toolbar has now changed and can
 be used to center the view. This is functionnally equivalent
 This works for all platforms The keyboard equivalent is
 to press on the "Home" Key (for Mac users, note that
 the HOME key is at the right of the help key its symbol
 being one arrow pointing to the top left).
  
-The Provenance icon (question mark) in the Toolbar
 now returns the X Y Z coordinates and Bfactor of the
 selected atom in addition to the layer, residue name 
 number and chain. 

-You can access a BLAST server. Select the residues to compare
 and use the corresponding item of the Edit menu to blast 
 against ExPDB or SWISSPROT. Results appear in a window
 where each word in red is in fact an hyperlink
 
-The text window has now more hyperlinks activated.
 You can access PROSITE definition files, SWISSPROT
 entries or directly load PDB or ExPDB files.

-A red/green stereo mode is now possible when openGL
 is enabled. This works best in wireframe. I will refine
 this mode later for solid rendering and for the faster
 non openGL mode.
 
-There is a new rotamer library derived by SC Lovell,M Word
 JS Richardson and DC Richardson.
 [The penultimate Rotamer Library; Prot Struct. Func and Genetics 40]
 It is located in the usrstuff directory and name
 Rotolib2.aa
 The previous rotamer library has been named
 Rotolib1.aa
 To make one of those rotamer lib current, make a copy
 of it and name it Rotolib.aa (by default Rotolib1.aa)
 I will design a clever way of switching among rotamer
 libraries later, as more libraries will come.
 All the new rotamer libraries are backbone dependent
 This means that when you mutate, the local backbone
 geometry is analysed and that rotamers are selected
 among "helix" "strand" or "coil" rotamers.
 The display in the toolbar is modified and looks like
 this:
 
 R:1/5 s: -3 p:0.41 h/h
 
 meaning Rotamer 1 out of 5 has been selected
 its score is -3 (the lower the better, as explained
 in the Manual)
 probability of finding this rotamer of 0.41, in other words
 it is like that in 41% of the cases.
 local backbone structure is helix and helix rotamers are used.
 
