R-Sym statistics in solved structures

From: Guillaume Gotthard
Date: 9 January 2012 10:28

Dear all,

Is there a mean to obtain statistics about R-Sym for deposited structures databases ?
I know it is possible for R-Free values but is it the case also for R-Sym ?

Guillaume Gotthard, PhD student
Biocristallography, Biotechnology and Structural Enzymology Group
URMITE Laboratory - UMR 6236 Faculté de Médecine
27, boulevard Jean Moulin

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From: Tim Gruene

Dear Guillaume,

I am not sure which database you refer to, but for every structure
deposited at the PDB since 2007, the data are available, too.

The PDB-header might report R_sym as should the publication.

Buy the whey, you should better get used to R_meas and consider R_sym as
deprecated.

Regards,
Tim

- --
- --
Dr Tim Gruene

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From: Eleanor Dodson


Dont forget Rsym and Rmerge are one and the same I believe..
Eleanor

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From: Ed Pozharski 

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

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From: Jacob Keller


Also R cryst is sometimes used for the same number, I think (of course
there are historical reasons for the different terms, but...).

JPK

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program