BRAGI: A Protein Visualization and Modeling Program

recent Pulication
Joachim Reichelt, Guido Dieterich, Marsel Kvesic, Dietmar Schomburg, and Dirk W. Heinz
BRAGI: linking and visualization of database information in a 3D viewer and modeling tool
Bioinformatics, Apr 2005; 21: 1291 - 1293.

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N E W S

• 06.11.2009: A new DEMO version of Bragi is released, time limited till 05.Mar.2010
  
  Fixed:
  Automatic replacement now works. It was totally screwed up
• 04.11.2009: A new DEMO version of Bragi is released, time limited till 03.Mar.2010
  
  Fixed:
  Several Bugs in the batch system.
  Note:
  new batch command: Cursor on|off
  new batch command(only Linux at now): Fullscreen on|off
  
• 20.10.2009: A new DEMO version of Bragi is released, time limited till 19.Feb.2010
  
  Fixed:
  A bug in HW-stereo display was found
  seg.faults in helpers were fixed.
  New:
  Changed to qt 3.3.8 on Linux, on Windows qt is static build in Bragi.exe
  Note:
  Linux compile is on openSUSE 11.1, 32bit and 64bit
  Windows is still on XP
• 18.04.2008: A new DEMO version of Bragi is released, time limited till 21.Feb.2007
  
  Fixed:
  Due to some changes in Windows we had crashes calculating any surfance New:
  Changed to qt 3.3.7 on SGI and Windows, on Windows now qt is static build in Bragi.exe Note:
  I'm sorry to inform you, but there is no further development in Bragi at now.
• 21.11.2006: A new DEMO version of Bragi is released, time limited till 21.Feb.2007
  
  Fixed:
  Automatic Replace could not be started at all.
• 07.11.2006: A new DEMO version of Bragi is released, time limited till 07.Feb.2007
  
  no new features, sorry
• 30.06.2006: A new DEMO version of Bragi is released, time limited till 30.Sept.2006
  
  no new features, sorry
• 17.02.2006: A new DEMO version of Bragi is released, time limited till 14.Apr.2006
  
  Fixed:
  Povray raytracing was buggy using tubes for the secondary structure
  New:
  We changed the format of the PDB files to match format 2.0. We now write out the element type of each atom (to our best knowlage)
  Note:
  Now BRAGI is lised on RCSB
  
• 05.12.2005: A new DEMO version of Bragi is released, time limited till 05.Feb.2006
  
  Fixed:
  You could not load files by double click or from within batch files, if there were spaces in the filename or in the path to it.
  
• 02.12.2005: A new DEMO version of Bragi is released, time limited till 02.Feb.2006
  
  Fixed:
  RMS-Fit did not move the molecules as it should.
  You may now use compressed XML files for saving and reading the status. This way you can use the status on any platform we support.
  Be aware, reading this file takes about 10 times reading the old status.
  
• 28.11.2005: A new DEMO version of Bragi is released, time limited till 28.Jan.2006
  
  Fixed:
  Replacing a residue was buggy.
  On Linux and Irix you are allowed to symlink the binary to an other directory.
  
• 01.11.2005: A new DEMO version of Bragi is released, time limited till 01.Jan.2006
  
  Fixed:
  Toggeling "Option Visible Secondary Structure" could make Lys and Arg to disapear.
  Calculating a surface in "solid fast" mode now works
  You can now export to vrml surfaces too.
  Note:
  The external helper "surface" was fixed. This is only in the packages
  
• 18.10.2005: A new DEMO version of Bragi is released, time limited till 18.Dec.2005
  
  Fixed:
  A bug in the rms fit routines.
  A bug in the call to extrenal programs, e.g. secondary structure prediction.
  New:
  We will switch the status file BRAGI uses to zipped XML. The file formats are automaticly recongnized on read. This needs a little more testing, so be carefull.
  And a bugfixed Qt-dll was here
• 22.09.2005: A new DEMO version of Bragi is released, time limited till 22.Nov.2005
  
  WARNING:
  We switched to QT 3.3.5, so you have to download an image!
  New:
  We implemented a new feature: Load a FASTA-Sequence file. BRAGI will perform a blast search to find known 3D structures. These structures may be dircet downloaded into BRAGI.
• 02.08.2005: A new DEMO version of Bragi is released, time limited till 02.Oct.2005
  
  Fixed:
  Bragi will hang on some batch commands
  
• 20.07.2005: A new DEMO version of Bragi is released, time limited till 20.Sep.2005
  
  Fixed:
  "Center and Scale" will optimize the size of the molecule to fit in x, y, and z into the display. Changed:
  Zooming in and out using the mouse is increased by a factor of 10 to match other programs. Fine zooming is aviable by pressing <CTRL><SHIF>, pressing the right mouse button and moving the mouse
  New:
  You can select objects and zoom/center to this using the context menu (right mouse button).
  Selecting residues in the ramachandran plot will center the 3D display to this residue.
  There is a new "Options" in the ramachandran plot to modify this.
• 11.07.2005: A new DEMO version of Bragi is released, time limited till 11.Sep.2005
  
  Fixed:
  Ramachandran plot was "disturbed"
  New:
  In ramachandran plot the meaning of single and double klick are interchanged
• 27.06.2005: A new DEMO version of Bragi is released, time limited till 27.Aug.2005
  
  Fixed:
  minor batch problems were fixed.
• 20.06.2005: A new DEMO version of Bragi is released, time limited till 20.Aug.2005
  
  Changed:
  Starting BRAGI from command line and giving a pdb file as option BRAGI will center all molecules.
  If you do not want this, use "-c "
• 24.05.2005: A new DEMO version of Bragi is released, time limited till 24.Jul.2005
  
  Fixed:
  Hardcopy no longer adds garbage at to, e.g. menu bars.
  Some left over debug messages removed.
  
• 11.05.2005: A new DEMO version of Bragi is released, time limited till 11.Jul.2005
  
  Fixed:
  Some features in batch scripts were not enabled or implemented.
  
• 03.05.2005: A new DEMO version of Bragi is released, time limited till 03.Jul.2005
  
  Fixed:
  The fix 05.04.2005 introduced a lot of problems. Please update!
  The apbs module to calculate electrostatics on surfaces now works as expected. There was a index swap. Be aware of memmory usage of apbs.
• 03.05.2005: A new DEMO version of Bragi is released, time limited till 03.Jul.2005
  
  Fixed:
  The fix 05.04.2005 introduced a lot of problems. Please update!
  The apbs module to calculate electrostatics on surfaces now works as expected. There was a index swap. Be aware of memmory usage of apbs.
• 12.04.2005: A new DEMO version of Bragi is released, time limited till 12.Jun.2005
  
  Fixed:
  Automatic replacement of sidechains did not work on Linux and Irix
• 05.04.2005: A new DEMO version of Bragi is released, time limited till 05.Jun.2005
  
  Fixed:
  There was a huge memory leak if molecules were deleted
• 17.03.2005: A new DEMO version of Bragi is released, time limited till 17.May.2005
  
  Fixed:
  During batch, the name of the molecule was "lost"
• 09.02.2005: A new DEMO version of Bragi is released, time limited till 9.April.2005
  
  New:
  You can now limit the surface to cube or sphere centered at any atome.
• 27.01.2005: A new DEMO version of Bragi is released, time limited till 27.Mar.2005
  
  Fixed:
  Redesigne of raytracing for povray 3.6. Surfaces looks really nice now.
  New:
  We added an interface to apbs (by Nathan A. Baker) to calclate electrostatics on the surface
  The Linux version is linked again system qt-lib. There should be no need to use StartBragi. On Linux start Bragi itself!
• 16.12.2004: A new DEMO version of Bragi is released, time limited till 16.Feb.2005
  
  Fixed:
  You could not read in surfaces. BRAGI crashed immideately.
• 15.12.2004: A new DEMO version of Bragi is released, time limited till 15.Feb.2005
  
  Fixed:
  SEQRES records are now written correct for all molecules, though they are not updated on exchange of residues.
• 30.11.2004: A new DEMO version of Bragi is released, time limited till 30.Jan.2005
  
  Fixed:
  
  The new MS-Windows version seemd to not run on many systems.
  I switched back to my old system for Windows compile.
• 25.11.2004: A new DEMO version of Bragi is released, time limited till 25.Jan.2005
  
  Fixed:
  
  FTP transfer passing a http style proxy should work now, as it shoul work without a proxy.
• 22.11.2004: A new DEMO version of Bragi is released, time limited till 22.Jan.2005
  
  HINT
  We switch to new computersystems.
  
  All newer versions are compiled on
  • Linux: SuSE 9.2
  • Windows: MS-Windows XP
  We do not support Windows 9x any longer!
  We do not support SuSE 8.x or gcc 2.xy-Systems any longer!
  
  Fixed:
  
  there was no way to rotate PHI of the second residue
• 04.11.2004: A new DEMO version of Bragi is released, time limited till 04.Jan.2005
  
  Fixed:
  
  The handling of floating text ("freetext") was really broken
• 21.10.2004: A new DEMO version of Bragi is released, time limited till 21.Dec.2004
  
  Fixed:
  
  The SGI Version from 11.10.04 crashed on exit due to a linker error.
  New:
  
  There is a set of test version included.
  These are Bragi-neu.exe
  and
  StartBragi.new
  Both use a different format to store the "status" and keeps a lot more data out of the PDB file
• 11.10.2004: A new DEMO version of Bragi is released, time limited till 11.Dec.2004
  
  Fixed:
  
  The Windows version crashed if trying to download files from RCSB, but the system is offline
• 01.10.2004: A new DEMO version of Bragi is released, time limited till 1.Dec.2004
  
  Fixed:
  
  artifacts if creation of splines/tubes falls
  memory corruption on filename creation during surface calculation
  minor syntax errors in the batch interpreter
• 20.09.2004: A new DEMO version of Bragi is released, time limited till 20.Nov.2004
  
  Fixed:
  
  memory corruption while calculating surfaces
  Modified:
  
  the cursor in the main graphics is now changed on keypress to indicate translate, roptate or scale
• 07.09.2004: A new DEMO version of Bragi is released, time limited till 7.Nov.2004
  
  Fixed:
  
  minor bugs in batch language
  highlighted CPK and sticks are allways shown
  Added:
  
  CPK may be shown even if related atoms are switched off
• 27.08.2004: A new DEMO version of Bragi is released, time limited till 27.Oct.2004
  
  Fixed:
  
  checking bonds/H bonds could kill BRAGI
• 20.08.2004: A new DEMO version of Bragi is released, time limited till 19.Oct.2004
  
  NEW:
  files from RCSB are downloaded to working directory, if the main directory for structures is not writeable (see FAQ)
  Fixed:
  
  sometimes there were funny binding from cofactors to solvent
  sometimes CPK of HETATM were not shown
• 19.08.2004: A new DEMO version of Bragi is released, time limited till 19.Oct.2004
  
  Fixed:
  
  The filedialog could add "(*" by mistake
  Making settings permanent could lead to a endless loop
  Deleting molecules could crash BRAGI
• 18.08.2004: A new DEMO version of Bragi is released, time limited till 18.Oct.2004
  
  Fixed:
  
  In the last version BRAGI did not highlight selection in InterPro and SwissProt dialogs
  You may build all crystallographic neighbours, not only a unit cell
• 13.08.2004: A new DEMO version of Bragi is released, time limited till 13.Oct.2004
  
  For Updates:
  
  Download at least bragi.exe AND bragi.set
  Fixed:
  
  Color by accessibe surface works again
  Color dialog ws not shown
  Connectivity check now works as expected
  RMS-Fits: now the selected molecules are moved, no other
  NEW:
  If Interpro information was not found, redirect to a direct search,
  this needs a little bit of testing
• 09.08.2004: A new DEMO version of Bragi is released, time limited till 9.Oct.2004
  
  Fixed:
  
  Connectivity calculation ignored a lot of connections
• 09.08.2004: A new DEMO version of Bragi is released, time limited till 9.Oct.2004
  
  For Updates:
  
  Download at least bragi.exe AND bragi.set
  Changed:
  
  BRAGI should now run from UNC pathes on Windows
  Fixed:
  
  In the unit cell there were several symetry equivalent molecules missing
  some stereo issues on sgi fixed
• 03.08.2004: A new DEMO version of Bragi is released, time limited till 6.Oct.2004
  
  Fixed:
  
  The Versiom 03.8.2004 had some buggy menus/dialogs
• 03.08.2004: A new DEMO version of Bragi is released, time limited till 2.Oct.2004
  
  Fixed:
  
  On Windows a resize of the "SwissProt"-Dialog could kill BRAGI
  On Windows the secondary structure calculation could fail, if pathnames were too long
  Several minor bugs on the DALI-suite
  You can now save the sequence in fasta format
  The "unit-cell" dialog seemed to hang forever
  BRAGI now shows the unit cell sourounding the selected molecule(s)
  Connections inside these molecules were fixed
  center all now works. We ignored Y and Z sizes
• 01.07.2004: A new DEMO version of Bragi is released, time limited till 1.Sep.2004
  
• 06.07.2004: A new DEMO version of Bragi is released, time limited till 6.Sep.2004
  
  Modified:
  BRAGI now can get files from RCSB through a proxy.
  
  • Linux/Unix: set ftp_proxy to something usefull:
    
    setenv ftp_proxy http://myproxy:1234
    or
    
    export ftp_proxy=http://myproxy:1234
  • Windows: use the IE settings to set the proxy. You must set the "Proxyserver" adress and port
• 01.07.2004: A new DEMO version of Bragi is released, time limited till 1.Sep.2004
  
  Fixed:
  Minor bugs in the RMS routines were fixed
  Minor bugs in the DALI routines were fixed
  If a DALI, SWISS-PROT or OMIM xml file is not found, a message box askes, what to do
• 29.06.2004: A new DEMO version of Bragi is released, time limited till 29.Aug.2004
  
  Modified:
  The "Tree View" was not only a little bit too large.
  Fixed:
  Free text bound to background was placed a little bit funny.
• 23.06.2004: A new DEMO version of Bragi is released, time limited till 23.Aug.2004
  
  Added:
  OMIM shows the disease too. Fixed:
  Reading a status file, the entries under "Sequence Tools" were missing.
• 22.06.2004: A new DEMO version of Bragi is released, time limited till 22.Aug.2004
  
  Tuned:
  CPK's in low res are up to ~8 times faster now.
• 11.06.2004: A new DEMO version of Bragi is released, time limited till 11.Aug.2004
  
  Fixed:
  Label setting via dialg works now even if same name is multiple times used
• 5.06.2004: A new DEMO version of Bragi is released, time limited till 04.Aug.2004
  
  Changed: Some databases are gzip'ed on disk now. (DALI and OMIM)
• 4.06.2004: A new DEMO version of Bragi is released, time limited till 04.Aug.2004
  
  Fixed:
  
  • Using Hardware Stereo right/left were toggled
  Added:
  
  • Direct link to the FAQ via "HELP"
  • Adjusting "Stereo angle" showns optimal viewing distance
  • You may preset your personal viewing distance in bragi.set. See

    BRAGI_STEREO_DIST=0.6
    			

• 10.05.2004: A new DEMO version of Bragi is released, time limited till 11.Jul.2004
  
  • 05.05.2004: A new DEMO version of Bragi is released, time limited till 3.Jul.2004
    
    Fixed:
    
    • Save settings fixed
    • Setting splines by a script
    Added:
    
    • Tubes colored by sequence
    • Create a movie of raytraced images
  • 26.04.2004: A new DEMO version of Bragi is released, time limited till 31.05.2004
    
    Fixed:
    
    • missing and corrected entries in bragi.set
  • 20.04.2004: A new DEMO version of Bragi is released, time limited till 31.05.2004
    
    Fixed:
    
    • batch setting of CA-Tubes
    • Hardcopies on SGI/IRIX
    • Rotate Bond: You may now select a residue by picking
    • Rotate Bond: No more nonbonded contacts inside the rotated group
    • CA-Tubes: Helices are now "flat"
    • Settings are ordered
    • Store only changed settings locally, preserve all previos settings
    • Menu for secundary structure changed
    • Logo is now fixed at right position, though it may be hidden by the menu
    • Pick in ramachandran graph highlights in 3D graphics
  • 02.04.2004: A new DEMO version of Bragi is released, time limited till 11.05.2004