Re: [ccp4bb] CASP ROLL needs your structures!

2013-01-19 Thread Ethan Merritt
On Saturday, 19 January 2013, Luecke, Hartmut wrote: > > In recent CASPs, there has been a shortage of new folds (according to PDB > exactly zero new folds deposited since 2009) and membrane protein targets. I have been wondering about that. It is true that the PDB has not listed any "new folds"

Re: [ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-19 Thread Edward A. Berry
Edward A. Berry wrote: http://www.computerhistory.org/revolution/timeline And this paper describes their use of a digital computer as if it were rather routine: Sternberg, J., Stillo, H. & Schwendeman, R. (1960). Spectrophotometric Analysis of Multicomponent Systems Using the Least Squares Met

Re: [ccp4bb] R-factors of various kind

2013-01-19 Thread U US
R = sum|(|(Fo)|-|(Fc)|)|/sum|(Fo)|. o=observed., c=calculated.Ri = sum|(|Io|-IIm|)|/sum(|Io|).m=mean, i=intensityRb =sum|(|Io|-IIc|)|/sum(|Io|). b=Bragg R-feeR-workR-symmR-rimR-mergewR (weighted) R-?R-?R-? Interrelation? Date: Fri, 18 Jan 2013 09:37:12 +0530 From: teriar...@gm

Re: [ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-19 Thread Edward A. Berry
http://www.computerhistory.org/revolution/timeline And this paper describes their use of a digital computer as if it were rather routine: Sternberg, J., Stillo, H. & Schwendeman, R. (1960). Spectrophotometric Analysis of Multicomponent Systems Using the Least Squares Method in Matrix Form. Anal

Re: [ccp4bb] Golden Jubilee of Ramachandran Plot

2013-01-19 Thread Jacob Keller
Were there really no computers in 1963? JPK On Fri, Jan 18, 2013 at 9:51 AM, David Schuller wrote: > > http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html > > Golden Jubilee of Ramachandran > Plot

[ccp4bb] CASP ROLL needs your structures!

2013-01-19 Thread Luecke, Hartmut
CASP* ROLL# *Critical Assessment of Structure Prediction #not a new sushi item In recent CASPs, there has been a shortage of new folds (according to PDB exactly zero new folds deposited since 2009) and membrane protein targets. The lack of such targets makes it problematic to reliably quantify th

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Edward A. Berry
Nat Echols wrote: On Sat, Jan 19, 2013 at 4:14 AM, Qixu Cai wrote: Could you please teach me any method to present the relationship between resolution and B values of all the x-ray structures in Protein Data Bank. Can the PDB statistics in RCSB do it? Perhaps, and I'm pretty sure PDBe has a s

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Pavel Afonine
Hi, or here, page 25: http://www.phenix-online.org/presentations/latest/pavel_validation.pdf Nat's plot is better though as it shows the spread. B-factor needs to be weighted by occupancy, I think. > - or show two plots: one for fully occupied atoms only, and the other one for partially occupie

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Huanwang Yang
Dear Qixu I am so sorry that I made a mistake. The webpage http://rcsb-auto-check.rutgers.edu/dev/pdbitem/index.html is under development and not available yet. The graph for B factor vs resolution is available http://rcsb-auto-check.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Huanwang Yang
Dear Qixu The RCSB has a webpage to show the statistics (the data populations and the correlation with the resolution) for all the annotated pdb data items. The current page is http://rcsb-auto-check.rutgers.edu/dev/pdbitem/index.html The graph that you need may be the one http://rcsb-auto-check

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Bryan Lepore
B-factor needs to be weighted by occupancy, I think. I think Moleman does it. -Bryan

Re: [ccp4bb] relationship between resolution and B values

2013-01-19 Thread Tom Oldfield
Qixu Cai There is a service at the PDBe that allows you to plot a large number of statistical relationships, and download and get data relating to this analysis. If you follow this link... http://www.ebi.ac.uk/pdbe-as/pdbestatistics/ And select from the EDS Property : Wilson B-factor (it is

[ccp4bb] relationship between resolution and B values

2013-01-19 Thread Qixu Cai
Dear all, Could you please teach me any method to present the relationship between resolution and B values of all the x-ray structures in Protein Data Bank. Can the PDB statistics in RCSB do it? Thank you very much! Q. Cai