Hello Joel,
I'll send you something that I think is exactly what you want. Check the MyModel.py.
I use two scripts to model my stuff when I want to define my custom restraints. I use two scripts because parallel processing just doesn't like putting everything in one script, don't ask me why :x
The first is build_model.py and it's basically the main script that modeller uses. It has a few extra features but don't mind them.
The important lines are:
(number 11) from MyModel import MyModel
(number 123) a = MyModel(env,
This just imports and uses the MyModel class defined in the second script: MyModel.py. That second one has what you need. Basically it defines a new class:
class MyModel(loopmodel):
that inherits from loopmodel instead of automodel. It then has a function called special_patches that includes my restraints. That includes disulfide bridges:
self.patch(residue_type='DISU', residues=(self.residues['981:B'], self.residues['984:B']))
Take a look at the scripts and if you have any doubt just call back :)
Regards! João [ .. ] Rodrigues
(Blog) http://doeidoei.wordpress.com (MSN) always_asleep_@hotmail.com (Skype) rodrigues.jglm
On Mon, Nov 9, 2009 at 7:00 PM, Joel Tyndall joel.tyndall@otago.ac.nzwrote:
> Hi folks, > > > > I’m looking to generate a model with a disulfide constraint as well as loop > refinement. I am still getting my head around the python scripts. In the old > top files, one could do multiple things in the single top file. I can’t seem > to get past this issue with the python scripts. I can run things separately > but I am at a loss trying to combine them. I seem to be stuck with > > > > a = loopmodel(env,.... > > > > vs > > > > a = MyModel (having defined the disulfide patch > > > > Could someone help or direct me to the write web page. Is this the process > to actually run two separate cripts (generate disulfide then run loop > refinement? > > > > Many thanks in advance > > > > An example script would be awesome > > > > J > > > > _________________________________ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > http://www.researcherid.com/rid/C-2803-2008 > > Pukeka Matua > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >