Swiss Pdb Viewer Deep View - FAQ

 

 

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Deep View
Swiss-PdbViewer

FAQ: Frequently asked questions

General:

Linux related:

PC / MS Windows:

SWISS-MODEL:

 

Note: Some of the manual pages are in PDF format, you may need Adobe Acrobat Reader.

General top

  • How can I create pictures with SPDBV?

    You can export your current view either as TGA file [Save-Picture], which can be included in any text or graphics package. If you have problems to display TGA files in Microsoft office programs, you are most likely missing a filter (See: MS Word & PowerPoint).

    Alternatively, you may export a POV scene to be rendered with POV-Ray. See also "Printing.pdf" for details.

  • Can I display PDB files containing only C-alpha coordinates?

    DeepView has not been designed to display     PDB files containing only C-alpha coordinates, and there are no plans to implement this feature. One possible work-around (thanks to Jim Proctor for the tip) is to use "Maxsprout" to reconstruct the missing backbone atoms.

Linux top

  • Error in loading shared libraries: libMesaGL.so.3. ...

Why this
The simple reason for this is that the newer Mesa now uses different names for the libraries than those with which SPDBV has been linked with. Apparently they are now called libGL.so and libGLU.so instead of libMesaGL.so and libMesaGLU.so.

How to solve it
The new Mesa is completely backward compatible and should not harm SPDBV from working properly. So there is no need to install an old Mesa version.
Just a little hack is needed to get it work: if you can get root access to your linux box, make the following symbolic links from the new libraries to the old names:


ln -s  /usr/X11R6/lib/libGL.so.1.2.0 /usr/X11R6/lib/libMesaGL.so.3
ln -s  /usr/X11R6/lib/libGLU.so.1.2.0 /usr/X11R6/lib/libMesaGLU.so.3

then run  
/sbin/ldconfig

to make the system remember this changes.

(I assumed that the libraries are installed under /usr/X11R6/lib. If this is not correct, please adjust the above commands with the correct location.)

PC / MS Windows top

  • When installing spdbv, I get an error message "missing glu32.dll" or "missing opengl32.dll". What does it mean?

    This error message means, that OpenGL is not installed correctly on your system. If you are running an old version of Windows95, you should download and install the missing files from the Microsoft FTP server.

    In recent versions of Windows (98/XP/NT/2000/ME/XP) OpenGL is already included, and this error should not occur if windows is installed properly. If you have a graphics card with OpenGL acceleration, make sure you are using the latest drivers supported by the card manufacturer.

  • I can't include my saved pictures in TGA format into MS Word or PowerPoint.

    When saving pictures from the OpenGL display mode, DeepView will save pictures in Targa bitmap format (.tga). The default installations of recent versions of Microsoft Office do no longer include filters for TGA file formats. The necessary converters can be installed either form your installation CD, or downloaded for free at the Microsoft homepage: [Office converter pack for different versions]

SwissModel related top
  • I have problems displaying the SwissModel results with SPDBV. How can I receive the results without using email attachments?

    Normally, SwissModel will return the final model coordinates as e-mail attachments. If your mail program has problems opening these attached files, specify "plain ASCII" in the SwissModel submission form. Use a text editor to remove any mail header lines, before loading the results into SPDBV. See "Results.pdf" for details.

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