NMR models to define domain

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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byrjames
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Joined: 2018.04.03 19:26

NMR models to define domain

#1 Post by byrjames » 2018.04.03 19:41

Hi All,

I am attempting to use EOM2.0 to model a flexible C-terminal tail of an 180 amino acid protein. I would like to define a domain using an NMR model. The NMR pdb file has 20 different models and I am not sure how to prepare the data so that EOM can use one of these models and define a domain. Should I simply try to move one model from the NMR pdb into its own pdb file?

Any help is greatly appreciated!

Thanks,

J

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Hayds
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Location: EMBL, Hamburg

Re: NMR models to define domain

#2 Post by Hayds » 2018.04.04 11:35

Hi James,

the most straight forward thing to do is extract the representative model (usually MODEL 1) from the PDB file. Check the PDB entry to make sure the first model is considered to be the representative one of the ensemble. Then just use this as your input rigid body.

Although I have not tested this I assume that EOM will push ahead and only use MODEL 1 in a PDB entry, but best to be safe and remove all subsequent MODEL entries from the file.

Another option is to determine an average structure/model to use. This can be done using Xplor-NIH tools or within the program MOLMOL (and lots of other programs). Usually the problem with that is you need to subsequently perform energy minimisation as some bonds and groups become distorted.

Hope that helps :)

Cheers,

Haydyn

byrjames
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Posts: 3
Joined: 2018.04.03 19:26

Re: NMR models to define domain

#3 Post by byrjames » 2018.04.04 15:26

Hi Haydyn,

Thank you so much! I appreciate your time; this was very helpful.

Cheers,

James

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