Ah yes a new logo... But it might be of interest to hear in this forum what has happened to the CCP4 logo that used to appear on the PISA and Fold pages in acknowledgement of the support from the BBSRC on the underlying algorithms for these services.
It is only by acknowledgement of the contribution of projects such as CCP4 that we can establish a continuing funding stream for the improvement of scientific software. I distinctly remember that this was acknowledged by the presence of the CCP4 logo on appropriate pages in the old PDBe website. Surely there is still space for that acknowledgement too? Yours perplexedly, Martyn Dr Martyn Symmons Cambridge ________________________________ From: Gary Battle <[email protected]> To: [email protected] Sent: Thursday, 14 March 2013, 10:27 Subject: [ccp4bb] PDBe website update: What's new Dear all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new and improved tools and services. Our first website update of 2013 features: 1. A new weekly overview of new biology in the PDB 2. Improved searching of EMDB entries with rapid filtering of results 3. New features for visual analysis of EMDB entries 4. Improved pages with chemical-shift-validation information for NMR entries 5. Easy sharing of PDBe pages -------------------- 1. A new weekly overview of new biology in the PDB. You can now view instances of new biology in the PDB including Pfam families, GO terms and UniProt entries that appear in the archive for the first time. For example, this week’s release includes the first structure ever from a member of the "Alternative Oxidase" Pfam sequence family (http://www.ebi.ac.uk/pdbe/searchResults.html?display=latest&tab=xref). Note that two kinds of "new biology" are shown: cases where an existing Pfam family etc. maps to a newly released structure in the PDB for the first time, and cases where an existing PDB entry maps to a new entry in Pfam, GO, UniProt, CATH or SCOP. 2. Improved searching of EMDB entries with rapid filtering of results. We have made searching the EMDB easier by implementing search filters that enable you to rapidly narrow down the set of search results. Filters based on experimental details, journal, organism etc. can be applied when searching (http://pdbe.org/emsearch) or browsing the contents of the archive (http://pdbe.org/embrowse). 3. New features for visual analysis of EMDB entries. We have introduced several new features to aid visual analysis and validation of EMBD entries, including: * A volume-estimate graph that shows how the enclosed volume of a map varies with the contour level (e.g. http://pdbe.org/emd-5357/analysis). * A Fourier-shell correlation (FSC) curve used to estimate the resolution of single particle maps (e.g. http://pdbe.org/emd-5357/analysis). * A residue-based atom-inclusion chart that can be used to assess the quality of fit of PDB models to an EMDB map (e.g. * http://pdbe.org/emd-2017/analysis). * An image showing the overlay of any deposited masks on a map, that show segmentations or some particular feature of an entry (e.g. http://pdbe.org/emd-1206/analysis). (Note that not all features are available or applicable for all entries.) 4. Improved pages with chemical-shift-validation information for NMR entries. We have improved the presentation of information on the validation of chemical shifts with VASCO. The redesigned webpages now show statistics on the assigned chemical shifts, any referencing corrections and a list of atoms with unusual chemical shifts values (e.g. http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr). 5. Easy sharing of PDBe pages. Regular visitors of the PDBe website may have noticed some small changes to the headers of our pages. The new headers include feedback and sharing buttons on every PDBe webpage. If you want to share what you find on one of our pages with friends or colleagues, use the share button to post the URL on Facebook, Twitter, etc. or to email it. If you have suggestions for improvements, please let us know by using the feedback button. You may also have noticed our new logo. Based on a motif that is found at all levels of structure, we hope that our new logo will quickly become synonymous with the provision of high‐quality information about 3D molecular and cellular structure. Our new logo and guidelines for its use are available from our website at http://pdbe.org/logo As always, we welcome your comments and suggestions through the feedback button at the top of every PDBe webpage. Gary. -- Gary Battle Protein Data Bank in Europe (PDBe) http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
