[ccp4bb] relationship between resolution and B values
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
Re: [ccp4bb] relationship between resolution and B values
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 some way down this list) Then select from the second parameter : resolution (at the top). Click [Show Distribution] This will show you a 2D distribution of B-factor based on Wilson statistics and resolution. You can clarify the plot by dragging the max scroll bar in the plot to the left, and you can select/download the data if you click on the plot. This basically shows the same information as the png file from Nat Echols, but you can see there are many possible way at looking at the data from here. I would welcome any suggestions to improve this data representation. Regards Tom Oldfield 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 No virus found in this message. Checked by AVG - www.avg.com http://www.avg.com Version: 2012.0.2221 / Virus Database: 2639/5543 - Release Date: 01/19/13
Re: [ccp4bb] relationship between resolution and B values
B-factor needs to be weighted by occupancy, I think. I think Moleman does it. -Bryan
Re: [ccp4bb] relationship between resolution and B values
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.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.png Best, Huanwang On Sat, 19 Jan 2013 20:14:47 +0800, Qixu Cai caiq...@gmail.com wrote: 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
Re: [ccp4bb] relationship between resolution and B values
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.png Regard, Huanwang On Sat, 19 Jan 2013 11:18:19 -0500, Huanwang Yang hy...@rcsb.rutgers.edu wrote: 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.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.png Best, Huanwang On Sat, 19 Jan 2013 20:14:47 +0800, Qixu Cai caiq...@gmail.com wrote: 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
Re: [ccp4bb] relationship between resolution and B values
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 occupied. - or (perhaps better) simply filter out partially occupied atoms: given the amount of atoms in PDB that wouldn't hurt statistics. Just curious: how weighting by occupancy is done? Pavel
Re: [ccp4bb] relationship between resolution and B values
Nat Echols wrote: On Sat, Jan 19, 2013 at 4:14 AM, Qixu Caicaiq...@gmail.com 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 similar service, and there are probably at least a half-dozen other ways to get this information, but it's basically just going to look like the attached plot. (Although I'm not sure I trust some of the very-low-B-factor structures at low resolution.) -Nat It might be good to look as a function of year deposited, since this seems to be changing. Perhaps some of the low B-factors at low resolution were obtained with ancient programs, or B-factor was not refined at all? Gerard CD Kleywegt wrote: *** For details on how to be removed from this list visit the *** ***CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html*** well, i had a quick look at the data stored in QDB (gjk, acta cryst d52, 842-857) which shows that for 435 structures the corr coeff between resolution and average b is only 0.06, i.e. insignificant the only non-trivial correlate (using a 0.2 cut-off) is the percentage of secondary structure (makes sort of sense) with cc=0.20 in my other large-scale test, mentioned a couple of weeks ago, i found that essentially all temp- factor-related staistics are incorrectly correlated with measures of model accuracy (e.g., higher average b tends to be accompanied by higher accuracy !). average b is very strongly correlated with completeness on the other hand. i suspect that problems with data and/or restraints (rather than physics) are a major determinant of the temp-factors we calculate for our models ... --dvd On Thu, 4 Jan 2001, Yu Wai Chen wrote: *** For details on how to be removed from this list visit the *** ***CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html*** Dear all, Does any one know if there is any correlation between the overall B-factor of a structure in relation to its resolution? Are there any publications on this topic? Also is there any correlation between the extent of disorder in a structure and the R-factor/Rfree? Thanks. Wai -- === Yu Wai CHEN, Ph.D. .. email:y...@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel:+44-(0)1223-402148 MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc ** Gerard J. Kleywegt Dept. of Cell Molecular Biology Bolshevik University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
