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

[Sarah Kamel <sarah.kamel@aucegypt.edu>]

Dear colleagues & friends, 
I am currently out of office with limited accesses to my mail. I will be back on the 18th of May. 
Best Regards 

On 15May, 2021, at 5:12 PM, David Gae via modeller_usage <modeller_usage@salilab.org> wrote:

> Dear ZHANG Cheng,
>
> Have you read these sections?
>
>
> I believe the Model uses the Biso to write a restraint energy values. Thats what I always see from my built models. 
>
>
> 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 <45BA,3BDE,CD06">> 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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