[phenixbb] Preferred treatment of residues with no electron density

vellieux frederic.vellieux at ibs.fr
Tue Aug 20 00:02:09 PDT 2013


Personally, this is what I do: if there is for example a missing surface 
loop that I cannot build then there will be no atoms in the model but 
header cards to describe this. Otherwise, I know the "missing" residues 
are there so that I leave them at full occupancy and let the temperature 
factors climb to best model the poor/missing electron density.

This is what makes most sense to me. I know others do things differently.


On 20/08/13 00:12, Mark Saper wrote:
> What is the preferred method for handling missing residues or residues with zero occupancy, in terms of PBD submission?
> I see three options:
> 	Remove them from the model
> 	set occupancy=0 and flag in REMARKs 475 and 480
> 	keep occupancy=1 and allow the temperature factors to climb
> I have a disordered region in my molecule which I am restraining to a portion of a structure in which that region is well resolved.  There are several residues that have no density in the current refinement, yet I want to keep them in the model.  Suggestions?
> Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Department of Biological Chemistry, University of Michigan Medical School
> 3040 Chemistry Building  |  saper at umich.edu  |  +1 (734) 764-3353
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Fred. Vellieux (B.Sc., Ph.D., hdr)
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