Re: [modeller_usage] How to (partially) override model.patch_ss_templates() ?
To: Modeller Caretaker <>
Subject: Re: [modeller_usage] How to (partially) override model.patch_ss_templates() ?
From: Luca Jovine <>
Date: Wed, 28 Nov 2018 12:46:13 +0000
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OK, will try - although, because the Cys pairs are very close, it is probably faster to just swap connectivity on the graphics and then relax the structure…
Thanks, Luca
> On 28 Nov 2018, at 00:10, Modeller Caretaker <> wrote:
>
> On 11/26/18 2:22 PM, Luca Jovine wrote:
>> However I just tried what you suggested - shifting the
>> alignment so that one of the two Cys of a pair is no longer aligned
>> with the template -, but what happens is that the Cys pairs that I
>> specified as making an alternative disulfide using special_patches
>> are now not bonded
>
> You will probably need to experiment a little bit with different alignments. You'll need to be careful not to change the alignment so much that it implies a structure that is inconsistent with the disulfides you want to impose.
>
> Ben Webb, Modeller Caretaker
> --
> https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
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