Re: [ccp4bb] Validation reports for all X-ray structures in the PDB
Any chance validation reports will ever be made for obsoleted entries? Eric On Wed, Apr 16, 2014 at 1:01 PM, Gerard DVD Kleywegt wrote: > Hi all, > > You may not have noticed, but 19 March 2014 was VR Day - the day that new > style wwPDB validation reports for all X-ray structures were made publicly > available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 > > The validation-related files for individual X-ray PDB entries can be > accessed through the web sites and ftp sites of the various wwPDB partners. > Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for > instance: > > http://pdbe.org/1cbs > > you will see the "percentile sliders" displayed in the PDBportfolio widget > (http://pdbe.org/portfolio) on the right of the page. (Clicking the big > white arrow will start a slideshow of images related to this entry.) The > legend of the percentile-slider plot contains a direct link to the > validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/ > entry-files/1cbs_validation.pdf). > > If you are not yet familiar with these new style validation reports, have > a look here: http://www.wwpdb.org/validation-reports.html - in particular > the user guide may be of interest: http://www.wwpdb.org/ > ValidationPDFNotes.html > > If you want to download the full report (which lists all outliers for many > of the validation criteria, instead of just the worst 5 or the first 5), or > a graphic image of the percentile-slider plot, or an XML file with all > validation data in machine-readable form, go to the downloads page of any > X-ray PDB entry, either through clicking the "Downloads" link in the menu > on the left, or directly by going to a URL of the form: > > http://pdbe.org/1cbs/downloads > > The section labelled "Validation" of the table provides the relevant links. > > Note that sites that include PDBportfolio in their pages now automatically > display the percentile-slider plot and download link as well! To see this > in action, go to the EDS page (if any) of your favourite X-ray PDB entry, > e.g.: > > http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs > > Please send any comments, questions or suggestions on the new style > validation reports to validat...@mail.wwpdb.org > > Questions about PDBe-specific pages and services can be sent to > pdbeh...@ebi.ac.uk > > --Gerard > > --- > Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK > ger...@ebi.ac.uk . pdbe.org > Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk >
Re: [ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, I don't know why my posting about validation reports re-appeared several times. The mail headers show that all 4 came through the domain ouhsc.edu but why they would be resent to ccp4bb is not clear, nor why this only happened with my posting. --Gerard
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=4105ff6448d5bdbd51e474e89f5a06ee532f480bdcd7c0205ce5c6d91b48300e The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=032b800b3e9b3f00999a10131c588183b134c5a44c0c6d5dafd999b619326c1e you will see the "percentile sliders" displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfolio&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=66fbe101d6708d887924bdc5bf25021570f9885c97daf3d064f9f7258c3303ad) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=1e6916c73273cdcf0e20a5b7d4ff23d7961c1d97a12988b072d32fcec45e7570). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=fd35f5139833bb5700372d7bf5f2398f28706b2154d8bc1d907eef9e82ac517f - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=11887d82818aef793f525049cf3b75a603cecba6cb0d7351fb3122b50d963f5a If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloads&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=83fb53eb3391a94d7ad7de7d2fcd02804657e56c7c0b5fb8aa3d655715d9a966 The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=SybxPBBuwtF1%2BkyzbVqM24zfDv%2FlkGA%2BD7nn1MMA5Xo%3D%0A&m=AUP7jVYRUvj3FZhfQ%2BtKgvpOcxF9LKdiIrh%2FUUiXbGk%3D%0A&s=57e3ff9f13e2ce786081e6f02d66213a2911f3d14ba6003a495ea2d5dd9c1650 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=a4ec416976c036dba11dd2eba52f58ea7623cf9c77878158a2d68f57c854ea56 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=e31ebbe11650822dcddc95c8d732073824315aaa1ef0a85f6947ca3e78d08cfe you will see the "percentile sliders" displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfolio&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=bb14504b68d5ac31e4d37c4a21b543c89a6fe18fac33b6c8b54db86869a541dd) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=9cfce1c69787f7b3b8c7aed8266cbc1a2f80474cd3a0e092aa23b32b22482dcf). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=899dc883a72c9aefd1cfa143a8a33e2ecc7bc1a7b0e3b42563c71730ddb8d141 - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=696eccc3065b76804f94f1b2ec49a7deede7cfe02e2251290f6a6d246cbaedff If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloads&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=3777dd064f5a5c7afd82c5e78bf77dc52fd85428c524d2083cd96316c6ff3527 The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=kNv1axZJB3LV6HLWWpBj9Gg%2BYIu0FLSw%2BlGFJs7MNAQ%3D%0A&m=QTxxFbNkBT%2FAcXlNDp2%2F%2FAqBPtkQyunnzjhGCmsBq2c%3D%0A&s=f8067c0121d03f420ec913cd927ad5a65c0bc1831b03ed4e43197317a3228336 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=494f114fbff8c5913722a563f0fac87daa91b4a0943e65f0c0d0258697324e71 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=ceb8a826f9fd1bcb945c2d5d2108bfcd5af42fb57dd42c876d8e434f7e44302f you will see the "percentile sliders" displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfolio&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=c36bb823c5eab11a764ba159a174b979be73b6a5afb1bdcd821b991dd813850d) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=09ba089e02bd4ac32ff47acb46f1659bfc50fd8dbf4b0064917cc1622f5bc36f). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=30a7f6e1086c7cf681d793b223a5f56a794439dc12a51b952b7ee69db0dfd24f - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=8384ec2de5f88f578d48e541831c47161606776d3787393f20fc9c6a59d4 If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloads&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=0af71922028784db5dee672128cc8d1a9131aba3b56f4777dc2bcbaa15c96a2c The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=ftLbjJYpc5s5JQz9Q6qd7uT7FxPLb4V0aIwH4RJhyZU%3D%0A&m=64lMZFiU8awh6xW6wpPoMU62Ujnj1YCzR74YPRJUaT4%3D%0A&s=4fe494878b502d19dedc40a0cfdeded207b166ca483a0d06643466303b4146b5 Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=ae7f982d2df966a2f95f73a794d46efffb16c227a75389fdd058f5cc62d1654d The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=eaa2ef06948e08de06b7fbd47cbfe0ec2c5dac82a4c70b2ffd055bbdf10311ec you will see the "percentile sliders" displayed in the PDBportfolio widget (https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/portfolio&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=106d86fcfd3fb5e631ca04b4d6f0be2adb8a60edf33ca698248517e47de9e5c7) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case https://urldefense.proofpoint.com/v1/url?u=http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=455ace0917c519ea7f631e3906413c60cf63deb9c4512491003cebf397e148d0). If you are not yet familiar with these new style validation reports, have a look here: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/validation-reports.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=88f1dd8be8660e1657bae27e311478f5ed3dfbd2922c198277688efbe98e7ba1 - in particular the user guide may be of interest: https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/ValidationPDFNotes.html&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=26d1c36fa29104dc85265fe4997ceaafec2e797dded7fb1ea2e39ae02988262a If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: https://urldefense.proofpoint.com/v1/url?u=http://pdbe.org/1cbs/downloads&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=3f324c797061411513168635757d7fc61545406ac5203d849b72a712bbe5e644 The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: https://urldefense.proofpoint.com/v1/url?u=http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode%3D1cbs&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=%2FDhb3m8fv4qGnCY3Ije8R1tn6gAt5pVYeiDZ56EjoJg%3D%0A&m=yPA4xaEOsseDoEa2EIY6DSEesNi330pMdsUc6fNMpOs%3D%0A&s=3f50278f4e3251a6c6efc1d0f293bed530f5fb4bcd94ef2a6426d1fbcffdfc7c Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Validation reports for all X-ray structures in the PDB
Bonjour Philippe, The reports are based on the recommendations of the wwPDB X-ray validation task force - see http://www.wwpdb.org/workshop/2011/index.html and the report published by this task force at http://www.cell.com/structure/abstract/S0969-2126%2811%2900285-1 Of course, if you have specific suggestions for improvements, we'd be interested to hear from you - feel free to mail them to validat...@mail.wwpdb.org A stand-alone server already exists - see http://www.wwpdb.org/validation-servers.html - hope this turns your Good Friday into a Great Friday :-) Best wishes, --Gerard On Wed, 16 Apr 2014, Philippe BENAS wrote: Dear Gerard CD/DVD/Blue Ray (;-) ), Yes, these new reports are great although they should/will improve over time. Another point that would be also really helpful would be to have the opportunity to run the associated scripts either locally or on a remote server from the PDB, prior to the submission itself. Hence they should provide strong guidelines the crystallographers during their rebuilding/refinement stages. I know Phenix for instance has already some of these tools, but not all. Could the PDB provide something in that way for the everyday use of a poor X-ray crystallographer ? Best regards, Philippe Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Gerard DVD Kleywegt ? : CCP4BB@JISCMAIL.AC.UK Envoy? le : Mercredi 16 avril 2014 19h01 Objet : [ccp4bb] Validation reports for all X-ray structures in the PDB Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: http://pdbe.org/1cbs you will see the "percentile sliders" displayed in the PDBportfolio widget (http://pdbe.org/portfolio) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf). If you are not yet familiar with these new style validation reports, have a look here: http://www.wwpdb.org/validation-reports.html - in particular the user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk Best wishes, --Gerard ** Gerard J. Kleywegt 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. ** Little known gastromathematical curiosity: let "z" be the radius and "a" the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: http://pdbe.org/1cbs you will see the "percentile sliders" displayed in the PDBportfolio widget (http://pdbe.org/portfolio) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf). If you are not yet familiar with these new style validation reports, have a look here: http://www.wwpdb.org/validation-reports.html - in particular the user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the "Downloads" link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads The section labelled "Validation" of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
