Patches/9v2

The patches below 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.

MODELLER (copyright © 1989-2026 Andrej Sali) is maintained by Ben Webb at the Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, Mission Bay Byers Hall, University of California San Francisco, San Francisco, CA 94143, USA. Any selling or distribution of the program or its parts, original or modified, is prohibited without a written permission from Andrej Sali. This file last modified: Wed Jan 28 17:10:30 PST 2026.