Hi Ibrahim!
I also found another package NAMOT (from Bill's website, thanks Bill); I
managed to install the package on MacOs PPC using fink.
However, I have a problem to run the program: issuing "namot" on the
command line starts the program for a second (flashing the Gui of Namot) and
returns the error: Creating shared mem segment: Cannot allocate memory
2800*700=1960000
I am sorry I missed this the first time around; I've been sucked into the
vortex of interminable intro chem teaching...
I've seen this bug a number of times and have filed a bug report. It is
hard to reproduce, but if you reboot it works. There is a real cockroach
of a bug that is harder to fix, however -- it messes up the phosphate
linkages between G and U I think.
I haven't however touched that program since Paul put an RNA builder in
Coot. If you have coot, go to
Calculate > Other Modelling Tools > Ideal DNA/RNA and you can generate an
A-form helix or a single strand of RNA, and then manipulate it to your
heart's content.
I hope that helps.
Bill
