Dear David,

Thank you for the information. I only get the PDB from my colleague, which has 0 occupancy values. The MODELLER can work with it.

I have not compared the occupancy of 0 and 1. It would be idea if Ben or developers can answer this.

So far, I only used "automodel" in the MODELLER.

Best Cheng

------------------&nbsp;Original&nbsp;------------------ From: "David Gae" <ddgae@ucdavis.edu&gt;; Date:&nbsp;Sat, May 15, 2021 11:12 PM To:&nbsp;"ZHANG Cheng"<272699575@qq.com&gt;; Cc:&nbsp;"modeller_usage"<modeller_usage@salilab.org&gt;; Subject:&nbsp;Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?

Dear ZHANG Cheng,

Have you read these sections? https://salilab.org/modeller/manual/node322.html

I believe the Model uses the Biso to write a restraint energy values. Thats what I always see from my built models. https://salilab.org/modeller/manual/node259.html#CMD:Selection.energy

It looks like R factor is considered from CIF file too.

Are you talking about partial occupancy or full occupancy with Xray structural file? occupancy and B-factors are related. Full occupancy the great the B-factor. is this the question you are asking here?

Also, have you tried to run occupancy of 0 &nbsp;on the PDB template versus occupancy of 1 on the PDB template and see if you get the same model?

This seem like an interesting question to look up.

Sincerely,David

On May 15, 2021, at 1:25 AM, ZHANG Cheng <272699575@qq.com&gt; wrote:

Dear MODELLER,

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?

I ask this because the Rosetta will ignore the lines with occupancy values of 0. I wonder if MODELLER does the same.

Thank you!

Yours sincerely Cheng _______________________________________________ modeller_usage mailing list modeller_usage@salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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?

------------------&nbsp;Original&nbsp;------------------ From: "Modeller Caretaker" <modeller-care@salilab.org&gt;; Date:&nbsp;Sun, May 16, 2021 00:39 AM To:&nbsp;"ZHANG Cheng"<272699575@qq.com&gt;;"modeller_usage"<modeller_usage@salilab.org&gt;;

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

On 5/15/21 1:25 AM, ZHANG Cheng wrote: &gt; The occupancy value is the&nbsp;57th-60th columns in the PDB file. Is this &gt; considered by MODELLER? For example, will a value of "0.00" or "1.00" &gt; 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

On 5/15/21 9:42 AM, ZHANG Cheng wrote: > Hi Ben, thank you for the confirmation. But since occupancy is not used > in modelling, I can simply consider it as not relevant?

Right. But don't take my word for it! This is easy to test by just changing the occupancy for some atoms in your template, rerunning the modeling, then comparing the output models.

> i.e. the > occupancy value will not affect the result?

It won't affect the coordinates at all, but any model atom that's aligned with an atom in your template will have the same occupancy value as in the template (any non-aligned atoms will get occupancy 1.0).

Ben Webb, Modeller Caretaker