Preferred treatment of residues with no electron density
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 | [email protected] | +1 (734) 764-3353
On Mon, Aug 19, 2013 at 3:12 PM, Mark Saper
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?
This came up a year or two ago, and someone (Ed Pozharski?) even did a simple survey. Support was roughly equal for options (1) and (3), with few people backing option (2) (zero occupancy). If the entire residue is missing, as opposed to just the sidechain, I would prefer (1), however. -Nat
Hello, 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. Fred. 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 | [email protected] | +1 (734) 764-3353
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