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

[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]

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]

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]

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.