Re: [modeller_usage] Introduction of Zinc restraints

[flavio seixas <>]

Hi Mehdi

I never used the restrains you listed before. I can not say if it is right or not. You may try to modeller and see the results by overlaying model and template (SSM superpose) in a graphic software like Coot.

My suggestion was more simple. I suggest you modify your alignment file.

You may have a lot of identical residues in the alignment of zinc finger region. Try to modeller them as rigid bodies, replacing then in your sequence by dots "."
 
This will copy the restrains of your template to your model.

Another suggestion is to do as Ben advised.

Regards,

Flavio


--- On Tue, 11/6/12, Mehdi Talebzadeh Farooji <> wrote:

From: Mehdi Talebzadeh Farooji <>
Subject: Re: [modeller_usage] Introduction of Zinc restraints
To: "flavio seixas" <>
Date: Tuesday, November 6, 2012, 2:29 AM

Hi Flavio

Thank you for your reply. I have to sets of restraints, the distance between SG of Cysteins and Zn 2.3 A, ND1 of his and Zn 2.0 A. I intruduced these restraints in MyModel.py

  class MyModel(automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        for ids in (('SG:204:B', 'ZN:238:B'),
                    ('SG:207:B', 'ZN:238:B'),
                    ('SG:225:B', 'ZN:238:B'),
                    ('ND1:228:B', 'ZN:238:B')):
            atoms = [self.atoms[i] for i in ids]
            rsr.add(forms.upper_bound(group=physical.upper_distance,
                                      feature=features.distance(*atoms),
                                      mean=2.3, stdev=0.03)

I am not sure if I am doing right thing.

Regards,

Mehdi

---

From: flavio seixas <>
To:
Sent: Sunday, November 4, 2012 9:07:58 PM
Subject: Re: [modeller_usage] Introduction of Zinc restraints

Hi.
try to build identical residues of zinc finger as well zinc atom as rigid bodies "." and modeler only the different residues.

Regards

flavio



------------------------------
Em sex, 2 de nov de 2012 18:41 GMT Mehdi Talebzadeh Farooji escreveu:

>Dear Users,
>
>I am trying to build a model of a Zinc finger protein, I am having problem with zinc coordination. Since the Zinc coordination residues of the model (CCCH) are slightly different from that of the template (CCCD), in the built model, the distances between atoms of the coordination residues and zinc do not match the standard zinc coordination. I was wondering if I could introduce the Zinc coordination restraints of the model in calculation. Any idea or help would be appreciated.
>
>Mehdi