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

["ZHANG Cheng" <>]

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

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

From: "David Gae" <>;

Date: Sat, May 15, 2021 11:12 PM

To: "ZHANG Cheng"<>;

Cc: "modeller_usage"<>;

Subject: 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  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 <" class="">> 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

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