Is occupancy value in the PDB considered for I-TASSER?

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lanselibai
Posts: 2
Joined: Sat May 15, 2021 10:09 am

Is occupancy value in the PDB considered for I-TASSER?

Post by lanselibai »

Dear I-TASSER,

The occupancy value is the 57th-60th columns in the PDB file. Is this considered by I-TASSER? For example, will a value of "0.00" or "1.00" have a different effect (e.g. weights) for the modelling?

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

Thank you!

Yours sincerely
Cheng
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: Is occupancy value in the PDB considered for I-TASSER?

Post by robpearc »

Is this the occupancy of the inputs template structures? If so I-TASSER doesn't consider this, but any residues that you desire may be removed from the template structures before uploading them.
lanselibai
Posts: 2
Joined: Sat May 15, 2021 10:09 am

Re: Is occupancy value in the PDB considered for I-TASSER?

Post by lanselibai »

Yes, I mean the occupancy value in the input templates.

I want the I-TASSER to build the homology model based on the template PDB I provide. So I choose "Option I: Assign additional restraints & templates to guide I-TASSER modeling." - "Specify template without alignment" - "Upload a structure"

You said "any residues that you desire may be removed from the template structures before uploading them". This is very worrying to me. Do you mean, the I-TASSER will NOT consider the template PDB because it has occupancy values of 0?
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: Is occupancy value in the PDB considered for I-TASSER?

Post by robpearc »

I-TASSER will consider the template structure without regard to the occupancy value. What I meant was if you don't want I-TASSER to consider a residue with an occupancy of 0, you may remove this residue from your template before uploading it.
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