Dear ZHANG Cheng,
Have you read these sections? https://salilab.org/modeller/manual/node322.html 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 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 272699575@qq.com 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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage