Re: [modeller_usage] Disulphide patch

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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