[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. **
[ccp4bb] CASP ROLL needs your structures!
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 the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Re: [ccp4bb] Golden Jubilee of Ramachandran Plot
Were there really no computers in 1963? JPK On Fri, Jan 18, 2013 at 9:51 AM, David Schuller dj...@cornell.edu wrote: http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Golden Jubilee of Ramachandran Plothttp://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Exactly fifty years from now i.e. in the year 1963, G. N. Ramachandran et. al published breakthrough original research in Journal of Molecular Biology. Ramachandran plot still remains a touchstone for protein form and structure (example, in validating a homology models). This plot is remarkable because it came ahead of time (it was proposed in 1963 when there were no computers, mechanical calculators were the cutting edge of technology) ... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Golden Jubilee of Ramachandran Plot
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. Analytical Chemistry 32, 84-90. Jacob Keller wrote: Were there really no computers in 1963? JPK On Fri, Jan 18, 2013 at 9:51 AM, David Schuller dj...@cornell.edu mailto:dj...@cornell.edu wrote: http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Golden Jubilee of Ramachandran Plot http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html Exactly fifty years from now i.e. in the year 1963, G. N. Ramachandran et. al published breakthrough original research in Journal of Molecular Biology. Ramachandran plot still remains a touchstone for protein form and structure (example, in validating a homology models). This plot is remarkable because it came ahead of time (it was proposed in 1963 when there were no computers, mechanical calculators were the cutting edge of technology) ... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu mailto:schul...@cornell.edu -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] R-factors of various kind
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...@gmail.com Subject: [ccp4bb] R-factors of various kind To: CCP4BB@JISCMAIL.AC.UK Hi, it would be nice if you highlight different type of R-factors used in the literature. I like to understand various kind of R-Factors, their mathematical formula, and relations among them.Thank you. Teri
Re: [ccp4bb] Golden Jubilee of Ramachandran Plot
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 Method in Matrix Form. Analytical Chemistry 32, 84-90. Well, not exactly routine by today's standards. I was going by memory- actual description is: The matrix inversions were . . . carried out on the MISTIC Computer at Michigan State University. The assistance of Susann Brimmer in carrying out the calculations on the MISTIC computer is gratefully acknowledged.
Re: [ccp4bb] CASP ROLL needs your structures!
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 since 2009, but that hasn't stopped people from publishing new structures and claiming they are new folds. Is this because there is no single recognized criterion for new in these cases? Or possibly the PDB hasn't updated their statistics since 2009? E.g. from the 1st page of Google Scholar hits for protein structure new fold 2RSXR Arai, S Fukui, N Kobayashi, J Sekiguchi - JBC 2012 Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold 3RX6R Banerjee, S Nath, A Ranjan, S Khamrui, B Pani, R Sen, U Sen - JBC 2012 A search of the Protein Data Bank using the DALI server (19) and PDBeFold (20) did not produce any significant match with the Psu structure designating it to be a new fold 2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011 Structure and genetic analysis of the arterivirus nonstructural protein 7α Ethan Merritt The lack of such targets makes it problematic to reliably quantify the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
