Is occupancy value in the PDB considered for MODELLER?
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
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
Dear David,
Thank you for the information. I only get the PDB from my colleague, which has 0 occupancy values. The MODELLER can work with it.
I have not compared the occupancy of 0 and 1. It would be idea if Ben or developers can answer this.
So far, I only used "automodel" in the MODELLER.
Best Cheng
------------------ Original ------------------ From: "David Gae" <ddgae@ucdavis.edu>; Date: Sat, May 15, 2021 11:12 PM To: "ZHANG Cheng"<272699575@qq.com>; Cc: "modeller_usage"<modeller_usage@salilab.org>; Subject: Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?
Dear ZHANG Cheng,
Have you read these sections? 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
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
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? > 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 > > 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 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
On 5/15/21 1:25 AM, ZHANG Cheng wrote: > 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?
No. Modeller reads the occupancy value for templates (you can access it as Atom.occ: https://salilab.org/modeller/10.1/manual/node388.html) but does not use it in modeling.
Output models will generally have an occupancy of 1.
Ben Webb, Modeller Caretaker
Hi Ben, thank you for the confirmation. But since occupancy is not used in modelling, I can simply consider it as not relevant? i.e. the occupancy value will not affect the result?
------------------ Original ------------------ From: "Modeller Caretaker" <modeller-care@salilab.org>; Date: Sun, May 16, 2021 00:39 AM To: "ZHANG Cheng"<272699575@qq.com>;"modeller_usage"<modeller_usage@salilab.org>;
Subject: Re: [modeller_usage] Is occupancy value in the PDB considered for MODELLER?
On 5/15/21 1:25 AM, ZHANG Cheng wrote: > 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?
No. Modeller reads the occupancy value for templates (you can access it as Atom.occ: https://salilab.org/modeller/10.1/manual/node388.html) but does not use it in modeling.
Output models will generally have an occupancy of 1.
Ben Webb, Modeller Caretaker
On 5/15/21 9:42 AM, ZHANG Cheng wrote: > Hi Ben, thank you for the confirmation. But since occupancy is not used > in modelling, I can simply consider it as not relevant?
Right. But don't take my word for it! This is easy to test by just changing the occupancy for some atoms in your template, rerunning the modeling, then comparing the output models.
> i.e. the > occupancy value will not affect the result?
It won't affect the coordinates at all, but any model atom that's aligned with an atom in your template will have the same occupancy value as in the template (any non-aligned atoms will get occupancy 1.0).
Ben Webb, Modeller Caretaker
participants (4)
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David Gae -
Modeller Caretaker -
Sarah Kamel -
ZHANG Cheng