There was huge changes between versions 3 and 4 in the way that GMT dealt with plotting degrees and degree formatting. I tend to use GMT 4 exclusively now, but on one of my work machines we have both versions installed (for backwards compatibility.) I had a problem recently trying to use GMT 3.4.5 with .grd files created by GMT 4.1.3. Specifically, the errors I would get were:

pstext: WARNING: DEGREE_FORMAT decoded (1) but is obsolete. Please use PLOT_DEGREE_FORMAT (ddd:mm:ss)
GMT Warning: Selected character encoding does not have suitable degree symbol – will use space instead
GMT Warning: Selected character encoding does not have minute symbol (single quote) – will use space instead
GMT Warning: Selected character encoding does not have second symbol (double quote) – will use space instead

I did a bit of searching, and it seems that these errors were caused by having only a .gmtdefaults file in my $HOME directory. The changes are so different between versions 3 and 4 that GMT has two different defaults files for the different version. I then ran the command

gmtdefaults -D > $HOME/.gmtdefaults4

and the errors disappeared. The -D tells the command gmtdefaults to print out the system defaults, -L would print out the user defaults (which I didn’t have yet).

but no $HOME/.gmtdefaults4 yet
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