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RasMol FAQ (Frequently Asked Questions) - A
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(Continued from previous part...)
How can I create the PDB file for a particular sequence?
May I strongly recommend that you consider using the Swiss-Model
server, written by Manual Peitche at the University of Geneva. This
e-mail and WWW server accepts as input either an amino-acid sequence
or a multiple sequence alignment with a protein of known structure
and performs comparative homology modelling to return the potential
3D structure to you by e-mail as a PDB file.
For more information visit the Swiss-Model WWW page at
www.expasy.ch/swissmod/SWISS-MODEL.html
I can't find the command line window in RasWin
This is a confusing problem with RasWin. When RasWin initially starts
under Microsoft Windows the command line window is initially iconised
(unlike the Macintosh or UNIX versions). The "RasMol Command Line"
icon appears at the bottom of the screen on the Windows background.
Unfortunately, this is often obscured by another window such as the
Program Manager or the File Manager. Both the "RasMol" icon and the
"RasMol Command Line" icons can be seen if all the open windows are
minimized.
A more convenient solution is to make use of the Microsoft "Alt-Tab"
control key combination. Hold down the "Alt"-key, and press the "Tab"
key one or more times until the name of the window you wish to bring
to the front appears, then release the "Alt"-key.
I get the message "No suitable display detected!"
This is a problem on the UNIX version of RasMol caused by one of
two potential problems. The first is that your DISPLAY
environment variable isn't set corrrectly or that you don't have
permission to display to the X Windows server. This can be
checked by testing whether it is possible to run any other X
Windows program.
The second problem is caused by a mismatch between the configured
version of RasMol and the display depths available on the current
X Windows server. This is most often the case when RasMol has been
compiled in 24/32bit mode (by defining THIRTYTWOBIT in either rasmol.h
or Makefile). The 24/32bit mode indicates that RasMol should use
3bytes/pixel (or 16 million simultaneous colours). If the current
X Windows server is unable to display this visual depth it reports
the "No suitable display" error. The visual depths supported by
the current X Windows server can be reported by typing the
"xdpyinfo" command. To solve the problem, recompile RasMol with
EIGHTBIT defined instead (i.e use one byte/pixel or 256 simultaneous
colours).
Note: that RasMol must be configured with EIGHTBIT for 1bit/pixel
(monochrome) or 8bit/pixel displays, with SIXTEENBIT for 16bit/pixel
displays and with THIRTYTWOBIT for either 24bit/pixel or 32bit/pixel
displays.
How do I create high resolution images in RasMol?
Unfortunately, raster images generated by RasMol are currently limited by
the screen resolution (though this defficiency is actively being worked on).
This means that images will generated at the resolution of about 72dpi
(dots per inch) even though must printers (including colour printers)
support resolutions of 300dpi, 450dpi or even 600dpi. This leads to
jagged bitmap like printouts where the individual pixels are often
visible.
The exception to the above rule is images produced in Vector Postscript
format using the "write vectps" command. These output files have
the advanatge of being generated at the printer's resolution, but the
disadvantage of not supporting all of RasMol's representations.
One way to minimise the limitations of screen resolution is to expand or
maximise the RasMol graphics window to the full size of the screen before
generating an output file. This ensures that the image contains as much
detail as possible. Another commonly used trick is post-process the image
in a graphics package such as PhotoShop or "xv" to expand and then blur
or smooth the images generated by RasMol.
See also the discussion on this topic in the
RasMol FAQ by Martz.
(Continued on next part...)
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