Depositing a new eCrystal

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Contents

Getting Started

Logging In

This is the home page for your eCrystals archive. From this page you can browse published crystal structures and manage your database.

To view embargoed records or upload a new structure you will need to log in with your user ID and password.


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Input your authentication details to access the deposit tools.


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Creating An eCrystals Record

Manage Deposits

After logging in you will be presented with the 'Manage Deposits' page, from here you can start to deposit a new record as well as review and administer current records in your archive by using the options on the tool bar.


To start a new eCrystals record, click [New Item].


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Initial Structure Deposit Name

Add a title for your eCrystal structure record.


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The Question mark [?] to the right, gives in-line guidance and advice on the 'Best practice' entries for each text box. By clicking the [?] box a drop down help appears with examples.


These tool tips can be found for every text entry during the deposit process.


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When you have completed the title box, click [next] to begin uploading your crystal structure files.


Uploading Files

To upload your CIF, click [browse]


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A standard file explorer box appears where you can browse your file system to select your CIF


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Your selected file appears in the dialogue box as the complete path, to upload this file click [Upload]


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Your CIF is now added to the record, to add the checkCIF output, click the [checkCIF] button and this will automatically send your CIF to the IUCr server for checking. The checkCIF output will be uploaded the the record automatically.


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Multiple File Upload

To upload further files to your record click the [Upload Multiple Files] box.


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The File selection box appears where you can drag and drop files into it or search for your files using the [add files] button.


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Highlight your files and press the [Select] button.


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This will then add your selected files to the upload list. To add these files to the eCrystals record press the [Upload File(s)] button.


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MOL File creation

We now need to generate the other files for your eCrystals record, like the MOL, CML and InChI files.

From the 'res' file click [Babel] and select the output format to be "mdl –MDL MOL format". Hit [GO]


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This will now write a MOL file and add it to your record


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CML Creation

Now we have the MOL file we can create the CML file, which will be used to display the structure using the Jmol Plugin.

On the mol file, select [Babel] Set the output file to CML – Chemical Markup Language, hit [GO]


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From the MOL file we can also generate our InChI string.


On the MOL file select the [InChI] button, this will run the InChI Generator script and upload it to your record.


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As we can see the InChI file has been generated and uploaded into your eCrystals record.


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By pressing the [Jmol] button a rendered interactive image will be displayed.


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Once all the files have been uploaded and generated, click the [Next] button to move onto the next stage of the deposit process, the details page.


Adding Sample Details

Author and Originator/Creator Details

Add creator/originator information in the text boxes. again drop down help is available from the [?] button on the right.

If there are more than four authors, click on the [More input rows] button.

The 'SC' 'DC' and 'SD' labels her mean:-

SC: Sample Creation DC: Data Collection SD: Structure Determination

Boxes should be checked next to the relevant author.


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Names and entries can be moved up and down the list by clicking the up and down arrow buttons to the right of the name.


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Compound Type and Formula

Select the crystal structure compound class and the empirical formula.


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The formula input uses Conventional 'mark-up' text to represent formulas.

For subscript use '~' eg C~4~ => C4

For superscript use '^' eg Li^2+^ => Li2+


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The InChI code will be automatically added if you generated an InChI file during the upload process.


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Keywords

Add all relevant keywords in the boxes below.

More input boxes can be obtained by clicking the [More input rows] button.


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By clicking the [?] help button the drop down help appears. On this you can click the 'here' text to get a list of approved keywords.


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Alternatively by typing into the text box, an auto complete function will begin to match words from the letters you have typed in. this works automatically after 4 letters have been entered.

When the list appears you can scroll down using the mouse and select the relevant word or phrase.


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Publication Date

This section deals with the publication date for your record, i.e. when it will be come public and available to the world.

You can either select the 'Publish immediately' check box or enter a future publish date.

The future publish date completes depending on your local laboratory policy, the Southampton policy is to make available, i.e. publish all our collected data after three years.


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Once all your information has been added click the [next] button to move on to the final deposit stage.


Review and Deposit

by clicking the [Deposit Item Now] button you move your record into the editor review buffer.

If you are an Editor within your eCrystals archive the record will be moved to the archive immediately.


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Once you have 'deposited' your record you can review all the information included as well as assess the abstract page.


Structure Details

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The Summary tab displays the abstract page for the eCrystal record.


eCrystals Summary

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Final Deposit

If after reviewing your data you have missed out some files or required information you can add these by clicking the edit tab and continuing with the upload process.

If you have completed the record upload you can deposit your structure by clicking the [move to repository] button and your record will be deposited into the live archive.


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Your record is now deposited !


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