AutoDep

Todo First

The 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 project

Once you have your CCPN project in the correct format (.tar.gz), it is possible to upload this file to the AutoDep server at PDBe.

On this page select "Start Submission" and then the option for "Based on a complete CCPN Project".  On this 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 EBI-1000) and your password on the "Continuation" option in the main AutoDep page.

Further details are given on the Upload page.

Initialisation and navigation in AutoDep

The first page allows you to specify details of the contact person doing the data deposition.  In AutoDep, there is a navigation frame on the left to move between different pages.  Completed pages are indicated with by a green button, whilst incomplete pages are shown with a red arrow head.  On each page, completed fields are marked by a green * and incomplete fields with a red *.

Fields that aren't mandatory have a "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 is virtually nothing left to finish in AutoDep.

Further details of this page and how to navigate in AutoDep are provided on the Initialisation page.

Instructions

On 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 Instructions page for more details.

Title and Authors

On 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.

Read more about this page in Title and Authors.

File Upload

The file upload page allows you to upload data files including structures, restraints, chemical shift lists, etc.  The § 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 upload page gives more detailed information.

Compounds and Sources

There 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 and Sources page for more details.

Sequences

This 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 [ligands/non std monomers].

Further details are given in the Sequences page.

Heterogens

On this page you can provide details of metal ions etc.

Further details about his page are given on the Heterogens page.

Samples and Experiments

This long page is for samples and experiments and allows you to provide details of solvents, sample components, NMR conditions, experiments and spectrometers.

Read more on the Experiments page.

Structure Calculations

On the same page as samples and experimnets, there is also a section at the bottom of the page to specify details of your structure calculation including software, method, conformers calculated and submitted, parameter used to select the best conformers and representative conformer.

Further details are given in the Structure Calculations page.

Other pages

After this page, there are a couple of short pages that allow you to (1) specify more details about your structure calculation software and (2) to indicate extra information about your structure (correct?)

There is a separate Other page to describe these stages of the deposition.

Preview

Finally you can see how your PDB header file will look.

An example is provided on the Preview page.

Validation and Submission

Then you should validate your submission.  If this completes correctly, you can submit your deposition to PDBe ????.  After the curators are satisfied with the structural aspects of your submission, you will obtain your PDB ID and the data will be forwarded to the BMRB for an ADIT-NMR submission where the NMR data can be curated.

There is a Validation page to describe this stage in more detail.