interpreting the comment of a reviewer

Mike Colaneri colaneri at MEDUSA.BIOC.AECOM.YU.EDU
Sat Aug 30 16:19:02 EST 1997


Dear colleagues,

	A colleague had the following comment from a reviewer:
"Figure ## is unnecessary; statistical indicators of overall map
quality are of more benefit than simply displaying a well-ordered
portion of structure."

	What does this reviewer write?

	Possibility 1
	Eliminate Fig. ## which is the electron density of an average 
region of the structure in its core and instead illustrate a statistical 
indicator of overall map quality such as the real space correlation 
coefficient with residue number?
	It is appropriate to write that the view that the colleague 
uses is the one most often presented in many structures of proteins 
from the same family, the portion of structure is representative of 
the family, and the specific structure I discuss is at 1.7 A resolution.
	Should the ordinate in the RSCC plot be from 0.0 to 1 as the 
O2D program plots and is seen in many papers, should it only cover the 
portion of the plot, or it is not an important point to even discuss, 
either way of presenting the plot being acceptable?

	Possibility 2
	Statistical indicators of overall map quality correspond 
to the refinement statistics that the paper already contains.
That is Rfree, Rwork, rms distance, average thermal factors, etc. 
Statistical indicators of overall map quality do not correspond
to the traditional map statistics and the reviewer does not ask
inclusion of the real space correlation coefficient plot.
	The reviewer asks to illustrate the map at the worst possible 
region of the structure, functional or not functional, stereochemically
important or unimportant, as compared to a representative region in 
order to illustrate the limitations in the map quality without 
illustrating the average map quality.
	Could one cite a paper in which the worst possible part of the 
structure is illustrated to evaluate map quality as compared to a 
representative region?  
	
	We would greatly appreciate all suggestions and opinions.
Thank you.

					Michael J. Colaneri




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