BRAGI: A Protein Visualization and Modeling Program

FAQ

1. Where do I get Bragi?
   • See http://bragi.helmholtz-hzi.de/downloads.html
   • Contact per E-Mail reichelt@helmholtz-hzi.de to get a licence.
2. How to enter the licence key?
   • Linux and IRIX
     Add to the system wide login scripts
     
     1. csh or tcsh
        add e.g. to /etc/csr.cshrc the line given in the email
        setenv ....
     2. sh or bash
        add e.g. to /etc/profile the two lines given in the email
        export ....
   • Windows XP
     Go to the properties of "My Computer"
     Select "Extended"
     Select "Environment"
     There are two block. Select on the lower one "System variables": New
     Enter Key name and Key value as given in the email.
     You have to logof and logon once
     Verify settings by:
     Open a Console (cmd.exe) and enter
     

     set

     and search for a line with

     BRAGI_KEY=...

3. What does it cost?
   • BRAGI is free of charge to academic users and, at now, for comercial usage too, but you have to sign a license agreement. Please fax the filled form to (49) 531 2612388
4. How do I make Bragi my default PDB-viewer?
   • Be aware, that the extension pdb is used in many applications, e.q. The PALM software is using it
   • On Windows: Open any Folder, select Extras->Ordneroptionen
     In the newly created Dialog select the third Tab “Dateitypen” and now search for the fileextension .PDB and .ENT, select each of them, click on “change” and then search for your version of BRAGI
   • On Linux using KDE:Start Konqueror, select “Settings”Konqueror einrichten” “Dateizuordnungen”...
     or see the documentation on plugger to add entries there. I have something like:
     Note: The lines are longer, so here I use "∼>" to indicate, that the line is continued!

chemical/x-pdb: pdb, ent: Protein Structure
    exits ignore_errors swallow(BRAGI): Bragi "$file"
    :internal:url
chemical/x-ras: pdb, ent: Protein Structure
    exits ignore_errors swallow(BRAGI): ∼>
        Bragi "$file" >/dev/null 2>/dev/null
    exits ignore_errors swallow(RasMol Version 2.7.2.1): ∼>
        RASMOL "$file" >/dev/null 2>/dev/null

4. How do I load a structure into BRAGI?
   • You have multiple possibilities to load a structure into BRAGI.
     • drag and drop a structure file (e.g. a PDB-file) on the Bragi executable icon.
     • use the menu bar FILE ->open
     • use the menu bar FILE->open recent)
     • link file extension (e.g. .ent or .pdb with the BRAGI executable. Then a double click on it will start a new BRAGI session
     • use shortcut >CTRL<O
5. Can I represent my structure in cartoon mode?
   • Select “Display Options”, “Calculate CA-Tubes”
6. How do I calculate a surface representation of my molecule?
   • Select “Toolbox”, “Calculate Surface”
7. How do I color my surface according to electrostatic potential, ...?
   • This is default, use this dialog to select the representation of the surface: electrostatics, hydrophobicity etc.
   • You may calculate the common surface for more than one molecule.
8. How do I center on a particular atom?
   • Click with the right mouse button on a residue and change selection mode to “atom”, double click on an atom and select “Center here”
   • Select from the menu bar Display Options->Center and select in the opening menu the atom
9. Can I make my molecular surface transparent?
   • Implemented in the Raytrace interface of BRAGI
   • This is not implemented in the normal graphigs of BRAGI at now, sorry.
10. How do I show only selected residues?
    • Not yet implemented.
11. How do I show atoms as van der Waals spheres?
    • This is called CPK in BRAGI. Select the desired Atoms using the mouse or use the hierarchical view to select them
    • Press the right mouse button, select “Set”, “Set CPK”
    • or
    • Select from the menu bar “Display Options”, “CPK/Balls/Stick” and set your own representation, than press “Set Selection”. To change these representations, there is no need to remove the CPK or sticks.
12. Can I combine different types of depictions (ball-and-sticks, ribbons, v.d.Waals)?
    • There are no known limitations in BRAGI
13. Can I renew images?
    • Not yet.
14. Can I use BRAGI with Windows? Does it work stable?
    • Yes, but you should have:
      • Windows XP Servicepack 1
      • Windows 2000 Servicepack 4
      • Windows 98 SE, with all patches as on October 2003
15. How can label an residue or atom?
    • To set the label mode, select “Selections”, “Pick Residues” or “Pick “Atoms”, then
    • Doubleclick on the residue or atoms you want to label and then press the right mouse button, select “set”, “Label”.
16. How can I see the molecule in stereo?
    • Select from the menu bar “Display Options” “Stereo Dual View” for side by side stereo or press “CTRL-F8”
    • Select from the menu bar “Display Options” “Stereo ZScreen” for top by button stereo or hardware stereo or press “SHIFT-F8”
    • Select from the menu bar “Display Options” “Projective” for no stereo or press “F8”
17. How do I find the molecule I want?
    • Select from the menu bar “Display Options”, “Center” and select the molecule you are looking for. Often it helps to decrease the scale too.
    • If this did not work for you, try:
    • Select from the menu bar “Display Options”, “Automatic Center and Scale All”
18. How do I display my molecule in BRAGI?
    • All molecules in are displayed immediately.
19. How do I download a molecule? (PDB file)
    • Select from the menu bar FILE->open->get Coordinates from RCSB. Enter a pdb entry code. This structure will be downloaded, if Internet is accessible, and saved in the demodata folder. That followed the structure will display in the 3D widget.
    • Note: BRAGI assumes to have direct ftp access to the Internet. There is now way to set a proxy.
20. How can I translate a molecule?
    • Use the mouse
      • If you got a middle button, press it and the molecules will follow the movement of the mouse
      • Press the “T” once, then press the left mouse button and the molecules will follow the movement of the mouse
    • Press “CTRL” and the arrow keys. This will translate the molecule to the direction the arrow
21. How can I rotate a molecule?
    • Use the mouse
      • Press the left mouse button and the molecules will follow the movement of the mouse. If you selected to translate by pressing “T”, press the “R” once to select rotation.
22. How can I scale the molecules?
    • Use the mouse
      • Press the right mouse button. Move the mose to the right and to the left to adjust the scale.
    • The “+” and “-” keys may be used to change the scale.
23. How to change the “slab” (thickness of the visible region)
    • Use the mouse
      • Press the right mouse button and the “CTRL” key simultaneous. Move the mouse to the right and to the left to adjust the slab.
    • Press “CTRL” and the “+” and “-” keys to change the slab.
24. How to change the size of labels
    • Use the mouse
      • Press the right mouse button and the “SHIFT” key simultaneous. Move the mouse to the right and to the left to adjust the size of the labels.
    • Press “SHIFT” and the “+” and “-” keys to change the size of the labels.
25. What is a “status” in BRAGI
    • The actual session is dumped to a file.
    • To read it in later you have to
      • restart BRAGI with the filename as the only option, e.g.
        Bragi -s status.status
        or
      • Use “drag 'n drop” to load this file: Drop it on the file icon of BRAGI or into a newly started session.
    • You may exchange a status file only on Windows and Linux (Intel 386 compatible systems only) but not between other systems. In the later case BRAGI may crash or produce garbage.
26. BRAGI and the Internet
    • To access to Internet using a http://... url BRAGI honors the environment variable http_proxy. BRAGI uses the usual Linux syntax e.g. http://proxy.localnet:1224
      This tells BRAGI to use the host proxy.localnet and the port 1224. Please ask your firewall admin for details. You may add a line to the file bragi.set:
      http_proxy=http://proxy.localnet:1224
27. How to select a database for the blast search
    • Goto Help->Settings
      • look for “Set database for BLAST Query”
      • Double click it and enter a valid database, at now one of:
        1. nr
        2. swissprot
        3. pdb
        4. month
        5. pat
      • Press three time <return>
28. How to configuer automatic download of structures?
    BRAGI can downlaod structures from a server Selecting "File" "Open" "Get Coordinates form RCSB" works in this order: I assume you entered e.g. "1aBc" as the 4 letter code, replace it with your own! First BRAGI searches the local storage for a file called "pdb1abc.ent"
    1. in the directory you started from
    2. in the directory where "BRAGI_STRUC_DIR" points to
    3. in the directory where "HOME" points to (Linux/Unix)
       or in the directory where "APPDATA" points to (Windos NT, XP)
       or in the directory where "TEMP" points to (Windos 9*)
    If found BRAGI ask to use this file and not to download it.
    If not found or forced to download, BRAGI will
    
    1. get the file "pdb1abc.ent.Z" form the server/directory "BRAGI_RCSB_FTP"
       in this case: ftp://ftp.rcsb.org/pub/pdb/data/structures/all/pdb/pdb1abc.ent.Z
       to
       • the in the directory "BRAGI_SAVE_PDB_TO" points to, if writeable, else
       • the in the directory you started from, if writeable, else
       • the in the directory "HOME" points to, if writeable (Linux/Unix)
       • the in the directory "APPDATA" points to, if writeable (Windos NT, XP)
       • the in the directory "TEMP" points to, if writeable (Windos 9*)
    2. call gzip -d for this file
    3. read in this file
29. Is there any way to display sequence conservation on the surface of a protein?
    i.e. to use the info I have in a sequence alignment.
    • The Espript server is the easiest way I know. Go here
      http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi
      choose Execute then Expert mode. Supply an alignment and a supplementary pdb file then execute. You get back an annotated alignment + the pdb file with a conservation score in the b-factor column. The only trouble can be making that the top sequence in your alignment matches exactly the sequence of the structure (no missing loops etc). You can read this new pdb file into BRAGI and select
      Colours
      Colour by Temperature Factor
      Idea: Daniel Rigden , see http://sourceforge.net/mailarchive/forum.php?thread_id=4325665&forum_id=60
30. Known problems
    • BRAGI may connect atoms in a funny order, if the topology is unknow for it, e.g. GTP in 2RAP
    • BRAGI uses temporary storage.
      On UNIX/Linux this are /tmp and /var/tmp
      On Windows this is %TEMP%
    • If residues got funny connections, you may remove the topology of this residue in .../topologie/
      e.g. if GTP is shown wrong, remove .../topologie/GTP
      this is due to different namings convention in RCSB
31. Known problem on Windows
    • Some tools build into BRAGI use scripts. These scripts do not run on Windows if BRAGI is started using the so called UNC notation, e.g.
      \\server\Bragi-Service\Bragi
      Workaround:
      Connect this share to a drive.