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.nz> wrote:

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

 


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