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Re: [modeller_usage] How to make better conformational sampling of models using MODELLER?
- To: Mahesh VELUSAMY <>,
- Subject: Re: [modeller_usage] How to make better conformational sampling of models using MODELLER?
- From: Modeller Caretaker <>
- Date: Thu, 25 Jan 2018 11:59:42 -0800
On 1/25/18 10:14 AM, Mahesh VELUSAMY wrote:
It was mainly performed to know how changing random seed
influencing on conformational sampling ?
Changing the random seed has no influence on sampling. It merely results
in different initial randomized structures, before sampling.
when I aligned all the models against top model (DOPE
SCORE) there was no variations on the backbone conformation and also in
terms of RMSD.
Modeller restrains the backbone to match your template(s), so this is
expected.
Is it possible to produce models in modeller that will have more
variations on the backbone and in terms of RMSD ?
Sure, by weakening any homology-derived restraints. Either adjust the
weights, or provide an alignment with lower sequence identity.
Ben Webb, Modeller Caretaker
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