On 7/13/11 1:15 AM, MUSTAFA BUGHIO wrote: > This is with reference to the python file > ***examples/commands/patch_disulfides.py > http://salilab.org/modeller/examples/commands/patch_disulfides.py i am > building a model with two disulphide bridges position: > *138 CYS -> 152 CYS > 198 CYS -> 209 CYS > where as the python file contains example for one disulphide bridge, how > can i edit the file or there is any other procedure to solve this > problem. Should i use above mentioned py file or patch.py for assigning > developing disulphide bridge.

This example auto-detects disulfide bridges - it looks at the template (in the case of patch_ss_templates) or the model (patch_ss) and simply looks for all pairs of Cys SG atoms that are close, and assumes there is a disulfide there. That's not what you want if you have a specific list of disulfides to restrain. In that case you would simply use the patch() command directly. See http://salilab.org/modeller/examples/commands/patch.py for a standalone example or http://salilab.org/modeller/9.9/manual/node24.html for one in combination with automodel. For multiple patches, you just call the patch() command multiple times.

Ben Webb, Modeller Caretaker