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An Information Portal to Biological Macromolecular Structures |
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Validation & Deposition Services Home | ADIT Home |
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An Information Portal to Biological Macromolecular Structures |
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PDB Home |
Contact Us
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Validation & Deposition Services Home | ADIT Home |
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Questions, comments, and suggestions about data deposition and processing should be sent to help@deposit.rcsb.org.
This server provides examples for depositing structures to the PDB using ADIT. The first two demonstrations will show how to use the ADIT Editor using partially loaded depositions. The third demonstration allows the user to upload files and practice depositing structures.
A tutorial guide for using all of the available ADIT functions is available at http://deposit.rcsb.org/adit/docs/tutorial.html.
Structures can be officially deposited using the AutoDep Input Tool (ADIT) at http://deposit.rcsb.org/adit/.
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Example 1 presents a completed deposition entry using the structure 1QAV. The coordinate file has already been loaded for you. Several of the data items are already filled in. To practice using ADIT, select any of the categories in the left frame to to view the information included. Feel free to change or add data. These changes should be saved by selecting Save button in each category after making any changes. This information will then be displayed in the bottom frame when DISPLAY AS TABLE is selected. At any time you may view the entire entry by pressing the PREVIEW ENTRY button. After you have gone through the categories you wish to investigate, press the DEPOSIT button. You will be given a measure of the completeness of the entry and will be presented with a table showing all of the information in the entry. At this point, you may choose to further edit the entry or press DEPOSIT to finish the session. This will not count as an actual deposition to the PDB.
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Example 2 presents an incomplete deposition entry using the structure 1KIP. A coordinate file containing only the SCALE cards, CRYST card, and coordinates has already been loaded for you. To practice using ADIT, select any of the categories in the left frame to to view the information included. Feel free to change or add data. These changes should be saved by selecting Save button in each category after making any changes. This information will then be displayed in the bottom frame when DISPLAY AS TABLE is selected. At any time you may view the entire entry by pressing the PREVIEW ENTRY button. After you have gone through the categories you wish to investigate, press the DEPOSIT button. You will be given a measure of the completeness of the entry and will be presented with a table showing all of the information in the entry. At this point, you may choose to further edit the entry or press DEPOSIT to finish the session. This will not count as an actual deposition. Sample data items and detailed directions for this example are available.
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Example 3 allows you to upload your own structures into the ADIT Editor. The files used should be on the same machine that you are running ADIT from. To start an example ADIT session:
After you have gone through the categories you wish to investigate, press the DEPOSIT button. You will be given a measure of the completeness of the entry and will be presented with a table showing all of the information in the entry. At this point, you may choose to further edit the entry or press DEPOSIT to finish the session. This will not count as an actual deposition to the PDB. | ||||||||||||
Additional ADIT information and tutorials are available at http://deposit.rcsb.org/.