View source for ADIT-NMR

= ADIT-NMR =

== '''Introduction'''  ==

Since May 2007, PDB&nbsp;coordinate and NMR data deposition proceeds through the [http://deposit.bmrb.wisc.edu/bmrb-adit/ ADIT-NMR] server.&nbsp; Deposition of structure coordinates, chemical shift assignments and structure constraints is compulsory.&nbsp; Unless an NESG structure is being held as part of an external automated structure determination competition, like CASP or CAS-D, all deposited information is to be released immediately after final approval of the PDB or BMRB entries.

== '''Using ADIT_NMR'''  ==

Before starting ADIT-NMR, be sure to prepare your files for deposition accordingly using the standard NESG protocols for [[PdbBmrbDeposition|PDB and BMRB&nbsp;depostion]].&nbsp; Be sure that the sequence information in your coordinate file ''exactly'' matches the entire protein sequence (i.e., including tags), even if there are residues missing from your deposition.&nbsp; To avoid any confusion at a later date, it is recommended that you collect all final files in a separate directory within your structure determination project.&nbsp; Also, be sure to gather together all the sample information and biological information associated with your target; most of this information can be accessed through the [http://www.spine.nesg.org/ SPiNE] database. 

One initiates an ADIT-NMR session by providing your e-mail address and selecting either PDB&nbsp;or BMRB deposition.&nbsp; The user is immediately e-mailed a restart session ID, which 
allows the user to log out and restart a session at a later time.&nbsp; 

Next, experimental files (PDB coordinates, chemical shift assignments in bmrb 2.1 or 3.0 format, the final structure constraints concatenated in one file, NOESY spectral peak lists) are uploaded.&nbsp; There are precheck and validation procedures prior to the generation of a series of data entry pages and sub-pages (i.e., entry information, citations, molecular assembly, experimental descriptions, structure determination).&nbsp; An example of the ADIT-NMR data entry form is shown in Figure 1. 

==== Figure 1:&nbsp; An ADIT-NMR session  ====

For each field, proceed through filling the required boxes (indicated by red asterisks).&nbsp; Many fields have pull down menus, and the software remembers similar responses entered in other fields.&nbsp; When a field is complete, a green check appears; incomplete fields remain red.&nbsp; If any required information is missing, the user will not be able to complete the deposition.<br> 

When the user completes all sections of the deposition, it is recommended that a preview document is created for editing prior to depositing the entry.&nbsp;&nbsp; When the entry is deposited, the user will immediately receive a PDB or BMRB&nbsp;ID number. 

One the user has completed a session (either PDB&nbsp;or BMRB&nbsp;deposition), one can proceed to either BMRB or PDB and a new session is made populated with data from the old session.&nbsp; For example, users can complete the PDB deposition first then proceed to BMRB, or vice versa. 

Finally, collect your PDB&nbsp;and BMRB&nbsp;ID's and proceed to [[HarvestDB|HarvestDB]] to entry your final project into the [http://nmr.cabm.rutgers.edu:9090/gallery/jsp/Gallery.jsp NESG&nbsp;structure gallery].

== '''ADIT-NMR Tutorials and Documentation'''  ==

Click [http://www.bmrb.wisc.edu/deposit/adit_overview here] and [http://deposit.rcsb.org/depoinfo/print_nmr.html here] for documentation on ADIT-NMR from the&nbsp;BMRB and RCSB&nbsp;web sites. 

Click [http://deposit.bmrb.wisc.edu/bmrb-adit/docs/tutorial.html here] for a brief tutorials on ADIT-NMR. 

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--JimAramini- 03 Nov 2009