George, Remember that scattering from every point in the cell contributes to every reflection; the R-value is a global metric of agreement between the model and the data. Hence, calculating the R-value for a few selected residues is not a sensible thing to do, unless you want to ask how well your particular fragment explains the scattering from the entire crystal (which I'm guessing is not the case for a 23 amino-acid fragment).
If you're interested in assessing the agreement between model and map for a particular fragment, you might want to consider instead the real-space R value and the related real-space correlation coefficient. You might also consider some reading to help bone up on the basics: http://www.amazon.com/Protein-Crystallography-Eaton-E-Lattman/dp/0801888085 (a primer, and a shameless plug) http://www.amazon.com/Biomolecular-Crystallography-Principles-Application-Structural/dp/0815340818 (the detailed stuff; essential) Cheers, Pat Loll On 5 Jun 2014, at 11:10 AM, George Devaniranjan wrote: > Hi, > > First off I am pretty new to CCP4/X-ray crystallography so please bear with > me as I try to explain my question. > > I was looking at a protein structure from the PDB (let's say 1aho.pdb). > > I have the corresponding MTZ file. I wanted to calculate the R-factor for > some selected residues (lets say 17-40). > > I can calculate the R factor for the whole protein using the (MTZ + pdb file) > SFCheck tool. > > Is there a way to calculate the R-factor for a segment of the protein? > > I can generate a masked map using COOT as follows: > Extensions--> Maps--> Mask Map by Atom Selection (inverse) > But the result is a map and not a MTZ file > (the format I need for the next step SFCheck) > > I tried using NCSMask but it did not work out. > Could someone suggest where I am going wrong in trying to calculate R for a > small part of the protein? > > Thank you, > George --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
