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AutoDepContents
AutoDep allows you to submit your CCPN project for a structural deposition to the PDB database. It is web-page based and below are a list of the pages that are relevant for an NMR deposition. Most of the sections have separate links that give more information about each of the AutoDep pages. The First section describes how to get your CCPN project in the right format to upload it to AutoDep. Todo FirstThe first thing to do after saving your project in CcpNmr ECI with an "Entry" object is to tar and gzip the project into one file - further details of how to do this are given in this page.Upload of CCPN projectOnce you have your CCPN project in the correct format (.tar.gz), it is possible to upload this file to the AutoDep server at PDBe (EBI).On this page select "Start Submission" and then the option for "Based on a complete CCPN Project" on this main AutoDep page. On the CCPN-AutoDep page you can browse for your CCPN project. You will also need to add a password. You can always return to your submission if you take note of your submission ID (something like 39896) and your password on the "Continuation" option in the main AutoDep page. Further details are given on the Upload page. Initialisation and navigation in AutoDepThe first page allows you to specify details of the contact person doing the data deposition. In AutoDep, there is a navigation side bar on the left to move between different pages. Completed pages are indicated with by a green , whilst incomplete pages are shown with a red  . On each page, completed fields are marked by a green  and incomplete fields with a red  .
Fields that aren't mandatory have an "N/A" button next to them, that allows you to rapidly fill in that field if it is not relevant in your study. There is also a "Global N/A" button that auto completes all the fields that aren't mandatory in one click. The more information that you have added to your CCPN project, the less you will have to do in AutoDep. If everything is set to green in ECI, then there will be virtually nothing left to complete in AutoDep. Each of the text for the input fields has a link with a popup window giving brief help about what should be put in that field. Further details of this page and how to navigate in AutoDep are provided on the Initialisation page. Instruction to AutoDepOn the page after initialisation, it is possible to select when you want to release your data and any information for the curators of your data.Go to the Instruction to AutoDep page for more details. Title & AuthorOn the title page, you can specify basic information about your project including title, authors and keywords. This is followed by a short page that includes a radio button option to specify the software used for your structure calculation.The Title & Author shows a figure of this. ReferenceOn the reference page, it is possible to provide any citations of relevance for your study.The Reference page provides more information. SoftwareThere is a radio button on this page to indicate your structure calculation software including (1) CNS/CNX, (2) XPLOR or (3) OTHER. This is useful for AutoDep to know at this stage for standard depositions, so that it knows the file structure to expect when you upload files on the next page (as well as display the appropriate refinement view. Based on this field AutoDep will also extract relevant data from harvest files). However, for CCPN project uploads, this page has been frozen as AutoDep is expecting data to be in CCPN format.File DepositionThe file upload page allows you to upload data files including structures, restraints, chemical shift lists, etc. The "ยง" symbol indicates that this data is mandatory for a PDB submission. If you already have a structure and associated restraints (which are now mandatory), this page will be completed for you automatically.The File Deposition page gives more detailed information. Compound & SourceThere next follows a page that relates to the polymeric chains used in your molecular system ("MolSystem") and the biological and experimental sources associated with these polymers.See the Compound & Source page for more details. SequenceThis is then followed by a page that is for the polymeric molecules in your "MolSystem" including the sequence of each polymer with a database cross reference. There is a choice to say if you have sequence conflicts between the atoms in your structure compared with the database cross references. Finally you can specify any modified or non-standard residues in any of your polymers.Further details are given in the Sequence page. HeterogenOn this page you can provide details of any ligands, ions, etc. that are in your structure.Further details about his page are given on the Heterogen page. Experimental DetailsThis long page is for samples and experiments and allows you to provide details of solvents, sample components and concentrations, experimental conditions (such as temperature or pH), NMR experiments and NMR spectrometers.See a figure on the Experimental Details page. Structure CalculationsThis section of the Experimental Details page is a summary table about the statistics for your structure calculation.Further details are given in the Structure Calculations page. RefinementThis short page allows you to give more details about your structure refinement software including authors and any additional details about your structure refinement.Other AnnotationThis is the final page in an NMR deposition to AutoDep and allows you to add any additional remarks of relevance to your structure and also to annotate important sites in your structure such as catalytic, cofactor, regulatory, or metal-binding sites.Preview PDB HeaderFinally you can see how your PDB header file will look.An example is provided on the Preview PDB Header page. Validation and SubmissionOn these pages you can validate and submit your deposition where you will be awarded a PDB accession code.There is a Validation and Submission information page to describe this stage in more detail. After curation, you will then receive an ADIT-NMR submission to complete. |
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