[phenixbb] Preferred treatment of residues with no electron density
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 A. Saper, Ph.D.
> Department of Biological Chemistry, University of Michigan Medical School
> 3040 Chemistry Building | saper at umich.edu | +1 (734) 764-3353
> phenixbb mailing list
> phenixbb at phenix-online.org
Fred. Vellieux (B.Sc., Ph.D., hdr)
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