Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?

["ZHANG Cheng" <>]

Hi Ben, thank you for the confirmation. But since occupancy is not used in modelling, I can simply consider it as not relevant? i.e. the occupancy value will not affect the result?

------------------ Original ------------------

From: "Modeller Caretaker" <>;

Date: Sun, May 16, 2021 00:39 AM

To: "ZHANG Cheng"<>;"modeller_usage"<>;

Subject: Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?

On 5/15/21 1:25 AM, ZHANG Cheng wrote:
> The occupancy value is the 57th-60th columns in the PDB file. Is this
> considered by MODELLER? For example, will a value of "0.00" or "1.00"
> have different effect (e.g. weights) for the modelling?

No. Modeller reads the occupancy value for templates (you can access it
as Atom.occ: https://salilab.org/modeller/10.1/manual/node388.html) but
does not use it in modeling.

Output models will generally have an occupancy of 1.

Ben Webb, Modeller Caretaker
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