Also R cryst is sometimes used for the same number, I think (of course there are historical reasons for the different terms, but...).
JPK On Mon, Jan 9, 2012 at 8:47 AM, Ed Pozharski <epozh...@umaryland.edu> wrote: > On Mon, 2012-01-09 at 10:28 +0000, Guillaume Gotthard wrote: >> Is there a mean to obtain statistics about R-Sym for deposited >> structures databases ? > > 1. It's actually quite easy to do on your own if you want. This > one-liner will get you the Rsym > > wget http://www.rcsb.org/pdb/files/XXXX.pdb?headerOnly=YES -O - -q | > grep 'R SYM ' | cut -d: -f 2 > > just replace the XXXX with the uppercase pdb id. I don't know what kind > of statistics you want, but assuming that you are after resolution > dependence, you can do this > > wget http://www.rcsb.org/pdb/files/XXXX.pdb?headerOnly=YES -O - -q | > egrep 'R SYM |RESOLUTION RANGE HIGH \(' | cut -d: -f 2 | tr -d '\n' | > tr -s ' '; echo > > 2. Beware that for probably the majority of the records you will get > NULL as the answer. Using "R MERGE" instead of "R SYM" would result in > a better outcome. > > 3. In any event, this is, imho, rather pointless. Rsym/Rmerge strongly > depend on multiplicity/resolution cutoff, thus their values across the > PDB don't really tell you much. Maybe this is why the PDB report > generator does not even list it as the option under "Data collection". > > Maybe it's time for the PDB to start asking the depositors to provide > the Rpim instead. Well, maybe this is 10 years overdue. > > Cheers, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
