Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?
To: David Gae via modeller_usage <>
Subject: Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?
From: Sarah Kamel <>
Date: Mon, 17 May 2021 09:10:20 +0200
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 <> 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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