Hi George, The R-factor is an overall disagreement statistic, it can not be broken down in parts for bits of the structure. (in other words, you can not correlate parts of the model with a subset of the reflections in the mtz, as a non-crystallographer might think - all the electrons in the asymmetric unit contribute to the intensity of each reflection)
what you can calculate for parts of the structure is how well it agrees with the corresponding part of the map, and some of the structure validation programs output statistics like this, i.e. map correlation per residue. And you could then average this for the residues of interest I suppose. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 5 Jun 2014, at 17:10, 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
