Problem with .ps and .pdf results of UNAFOLD

3 replies [Last post]
ramsan
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Joined: 05/04/2012

Hi all,

I am a newbie to UNAFOLD/MFOLD and I need this clarification immediately. After I ran UNAFOLD for my RNA sequences on Ubuntu OS, I got the RNA secondary structures in .ps and .pdf formats. In .ps files the entire structures can be seen but the .pdf files have only a part of the structures. On Windows OS, both .pdf and .ps files show only part of the secondary structures. I need the complete structure in .pdf format. How can I get complete structures in .pdf files. Please help.

Thanks in advance,

Ramsan

zukerm
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Joined: 11/12/2010

I know exactly what your problem is and it is partly our fault. A PostScript file contains a line that contains "Bounding Box" information. A PostScript display program that reads and obeys the content of the Bounding Box line will give you a correct structure. Similarly, a program that converts PostScript files into pdf format will give a correct output only if the bounding box information is properly interpreted. It is our fault for using a non-standard page size (not 612pt×792pt, which is US letter size and close enough to the European A4 standard for display purposes). It is not our fault that stupid software ignores bounding box information. I'm not surprised that Windows OS gives the worst results.

The web site converts from PostScript to pdf properly, so all pdf files computed using the mfold or DINAMelt web applications should display properly. The PostScript files will be properly displayed only if the reader interprets them correctly. The problem is with the distributed package.

Try changing PostScript file names to end with ".eps" instead of with ".ps". That could cause a PostScript display program to display the image correctly. Similarly, it might cause some conversion programs to convert to pdf correctly. Another thing that you can do is to edit the third line of a PostScript file (you must open the file using a plain text editor) and replace
1 1 scale
by
0.64 0.64 scale
This is guaranteed to work. No user should have to resort to such methods, but I cannot offer a better solution immediately.

If you have "gs" (Ghostscript) running on your computer, which is likely, download my Unix bash script, myps2img.bash. Create a symbolic links:

ln -s myps2img.bash myps2pdf.bash
and

ln -s myps2img.bash myps2jpg.bash
and

ln -s myps2img.bash myps2png.bash
If you run
myps2pdf myfile.ps
then you will get an output file "myfile.pdf" that has been correctly converted. Similarly if you want to convert to jpg or png format. If you have the "convert" program, you can use it directly. Please let us know if you have success.

ramsan
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Joined: 05/04/2012

Thank you Sir for helping me out in this. Change of scale in PostScript file and your bash script worked like a wonder.

admin
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Joined: 09/23/2010

This will need to be looked into, but for now, I'd suggest simply converting the files from .ps to pdf format. If you don't already have something on your computer (doubtful), you can look up TeXShop, or just do a search for "free .ps to .pdf converter". Trust me, they're everywhere.

Good luck, and thanks for bringing this to our attention.