Patches/9v2

Patches on this page can be applied to Modeller 9v2 to fix some minor problems. (Use the Unix `patch` command, or apply them by hand.)

(!) The patches are listed in chronological order (oldest first), so you should apply them in this order to avoid problems.

• initial_malign3d.patch: make the INITIAL_MALIGN3D option work again with TOP scripts.
• loop_output.patch: set OUTPUT correctly so that TOP loop modeling scripts work.