Deposition Entry Completion Interface

Setup Deposition of Coordinate and NMR Data to PDB and BMRB

The popup version of CcpNmr Entry Completion Interface (ECI), available from Analysis in the Structure menu. With it, you can complete all the necessary information required for PDB and BMRB data depositions by adding an “Entry” object to your CCPN project. An “Entry” object contains all the information that you wish to deposit with your submission. You can also select chemical shift lists, peak lists, structural restraints, ensembles, etc. and all at the click of a button. In addition, you can add all the meta data that is required for submissions to the PDB and BMRB. This can be done securely on your desktop computer over the duration of your NMR project.

For more documentation see the ECI section of the PDBe pages at the EBI web site.

Main Panel

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Main

Add a new “Entry” and check the completeness of it

pulldown Deposition Entry: Name of “Entry” being edited, add a new one with the button at the bottom left of this tab

pulldown Molecular System: Name of molecular system used in the study - review it in more detail in the “Molecules” tab

entry Title: Title that will be in the header of the PDB file

pulldown NMR Method Type: Type of NMR data collected, choose from: solution, solid-state, theoretical or ?

pulldown Submission Type: Is the deposition for the PDB or BMRB? The mandatory fields in the completeness report below will reflect the type of deposition to be done

entry *None*: Keywords that will be in the header of the PDB file

button +: Add extra row

entry Text for a detailed description of your study (like a mini abstract)

entry Additional instructions or notes that you wish to convey to the curators about your deposition

Completion Report

Table 1
CCPN Data Type Indicates mandatory data items for PDB or BMRB depositions - clicking in any field will take you to the correct tab for editing the data (Editable)
Comment Has the mandatory data been completed? Finished data is shown in green. Clicking on any missing data (shown in red, orange, or yellow) will take you to the correct tab so that you can add this information (Editable)

button Add New Deposition Entry: Add a new “Entry” object that can be submitted to the PDB or BMRB

button Remove Current Deposition Entry: Remove the currently selected “Entry”

button Export as NMR-STAR 3.1: Export an NMR-STAR 3.1 file that can be uploaded in ADIT-NMR

button Export PDB Coords: Export coordinates in PDB format for viewing with Rasmol, etc.

People

Add people, group and address information

People

Table 2
# Number of the person in list
Entry Author? Is the person an author in the “Entry”? - toggle by clicking (Editable)
Contact? Is the person a contact person? - toggle by clicking (Editable)
Primary Contact? Is the person the primary contact used by AutoDep? - toggle by clicking (Editable)
Family Name Family name of the person (Editable)
Title Professional title of the person such as Dr, Prof, Mr, etc. (Editable)
Given Name Given name of the person (Editable)
Initials Any middle initials in the person’s name (Editable)
Family Title (e.g. Jr.) Family title of the person like Sr., Jr., III, etc. (Editable)
Group Group name that the person is attached to - add new groups in the frame in the bottom left of this tab (Editable)

button Add Person: Add a new person

button Remove Person: Remove the currently selected person

button Set Person as Author: Set the currently selected person as an “Entry” author

button Set Person As Contact: Set the currently selected person as a contact person

button Set Person as Primary Contact: Set the currently selected person as the primary contact

Group Information

Table 3
Group Name Name of the group
Mailing Address First few lines of the mailing address of the group (Editable)
City City where the group is located (Editable)
State/Province State or Province such as Cambridgeshire, CA or ON (Editable)
Postal Code Postal code or ZIP code (Editable)
Country Country where the group is located (Editable)
Organisation Type Type of organisation the group is attached to - from academic, government, commercial or other (Editable)

button Add Group: Add a new group

button Remove Group: Remove the currently selected group

Contact Person Information

Table 4
Family Name Family name of the person
Given Name Given name of the person
Email Address Email address of the person - add with the button below
Telephone Telephone number of the person (Editable)
FAX FAX number of the person (Editable)
Position Role of the contact person in the project - principal investigator, responsible person, investigator (Editable)

button Add Address: Add a new email address for the person selected - the person does need to be set to being in a group using the two other frames in this tab

button Remove Address: Remove the email address and other information for the currently selected person - note it will also remove the link to their group

References

Add citations and software used

Citations

Table 5
# Number of the citation in list
Type Type of citation based on the button used to add it
Submit? Is the citation to be submitted? Primary, other (for a secondary publication) or no (Editable)
Authors Add authors for the citation based on people added in the preceding tab (Editable)
Editors Add editors based on people added in the preceding tab (Editable)
Year Year of publication, only editable if the status of the citation is set to published (Editable)
Title Title of the citation (or title of any book chapters) (Editable)
Journal Abbrev The abbreviation of the journal’s name (only for citations in journals) (Editable)
Issue Issue number, only editable if the citation is from a published journal reference (Editable)
Volume Volume number, only editable if the status of the citation is set to published (Editable)
First page First page number, only editable if the status of the citation is set to published (Editable)
Last Page Final page number, only editable if the status of the citation is set to published (Editable)
Status Publication status of the citation - from published, in press, in preparation (Editable)
PubMed ID PubMed number, only editable if the status of the citation is set to published (Editable)
DOI Digital Object Identifier, only editable if the status of the citation is set to published (Editable)
Keywords Keywords used in the publication (Editable)
Details Additional information about the citation (Editable)
Book Title Title of the book (for book citations only) (Editable)
Book Series Book series (for book citations only) (Editable)
Book Publisher Publisher of the book (for book citations only) (Editable)
City City of book publishers, institution of Thesis or conference location (not relevant for journal publications) (Editable)
Country Country of institution of Thesis or conference location (not needed for journals and books) (Editable)
Institution granting Thesis Name of the institution granting a Thesis (Editable)
Conference Title Name of conference for abstract citations (Editable)

button Add Journal Paper: Add a new journal citation

button Add Book/Chapter: Add a new book citation

button Add Thesis: Add a new Thesis citation

button Add Conference Paper: Add a new conference abstract citation

button Remove Citation: Remove the currently selected citation

Software

Table 6
Name Name of the software used
Version Version number of the software
Tasks Choose a list of tasks that the software was used for during the study; such as peak picking, chemical shift assignment, data analysis, structure calculation, geometry optimisation, etc (Editable)
Vendor/Author Authors or vendors who produced the software (Editable)
Vendor Address Mailing address for the software authors/vendors (Editable)
Vendor Website Web address for the software authors/vendors (Editable)
Details Additional information about the software (Editable)
Method Method that the software uses to perform the task; mainly for assignment/peak picking strategies, or for structure calculation methods such as simulated annealing, distance geometry, DGSA, molecular dynamics, matrix relaxation, torsion angle dynamics, etc. (Editable)

button Add Software: Add a new software and version of the software

button Remove Software: Remove the currently selected software

NMR Data

Add chemical shift lists, peak lists and other NMR datasets

NMR Measurements

Table 7
Data Type Type of NMR data such as shift lists, peak lists, relaxation data, etc.
Available Number of lists in the CCPN projects for the specific NMR data type
Selected Number of lists selected for deposition to PDB/BMRB for the specific NMR data type
Notes Description of the NMR data type

button Add All Available NMR data: Rapidly select all available data lists for deposition to PDB/BMRB

button Remove All NMR data: De-select all data lists for PDB/BMRB deposition - at least one chemical shift list is now mandatory for all depositions

NMR Lists Selected for Deposition

Table 8
ShiftList Indicate the type and name of each list, based on list type selectd in the top frame
Name Name of list which can also be changed (Editable)
Size Number of data points in the list
Submit? Is the list selected for deposition? - toggle by clicking (Editable)
Software Software used to make the list - the software will also need a method selected in the References tab (Editable)

button Select All: Select all lists of the selected data type

button Select: Submit the currently selected data list

button Unselect: De-select all lists of the selected data type

button Unselect All: De-select the currently selected data list

Shifts

Add chemical shift references and look for chemical shift outliers

Chemical Shift References

Table 9
# The serial number of the chemical shift reference specification
Class Whether the chemical shift reference is internal or external to the sample
Isotope The kind of nuclear isotope to which the reference appliesThe number of experiments in the project which use the shift reference specification (Editable)
Experiments The name of the molecule used to give a reference value to chemical shifts
Mol. Name Which atom of the reference molecule provides the reference chemical shift value (Editable)
Atom The reference value of the chemical shift for the specified atom (Editable)
Value Which measurement unit the chemical shift reference value is in; ppm, ppb or ppt (Editable)
Unit Whether the chemical shift referencing is direct or indirect (and thus uses a shift ratio) - this field can be toggled (Editable)
Ref Type The precise numeric ratio used to indirectly get the reference shift value of an isotope, given the direct measurement of a different isotope (Editable)
Indirect Shift Ratio For external references, a description of the geometry of the container used to hold the reference compound - for example, cylindrical or spherical (Editable)
Sample Geometry For external references, a description of the location of the reference (Editable)
Location For external references, orientation of the reference container with respect to external magnetic field - for example, parallel or perpendicular (Editable)
Axis Documentation missing (Editable)

button Add Standard IUPAC References: Add standard IUPAC chemical shift references for 1H, 13C, 15N and 31P

button Add Internal Reference: Add a new record for a chemical shift reference that is internal to the sample

button Add External Reference: Add a new record for a chemical shift reference that is external to the sample

button Remove Selected: Delete the selected chemical shift reference records

Unusual Chemical Shifts

pulldown Shift List: Choose a chemical shift from the CCPN project

Table 10
# The serial number of the resonance
Isotope The nuclear isotope type of the resonance
Resonance The assignment annotation for the resonance
PPM Actual chemical shift of the resonance
SD Standard deviation of shift in multiple experiments???
BMRB Mean The average chemical shift for the atom type given in BioMagResBank data
Random Coil The sequence-adjusted random coil chemical shift value for the atom type

Molecules

Review the molecules, chains and unusual chemical components in your molecular system

Molecular System Chains

Table 11
Chain Code Code identifier for this chain
Length Number of residues in chain
Molecule Name of template molecule as shown in middle frame
Conformational Isomer For biopolymers or ligands, does the indicated component of the system represent an observed conformational isomer of another component of the system. For example, component one may represent a polypeptide chain with proline 34 in the cis conformation and component two may represent the polypeptide chain with proline 34 in the trans conformation. In another example, component one may be alpha-D-glucose and component two beta-D-glucose (Editable)
Chemical Exchange State A flag indicating whether the component of the system is in chemical exchange with another component of the system. Set as ‘yes’ if the component is in chemical exchange with another component in the system - for example ligands that are present in both the free and bound states (Editable)
Folded State An enumerated list of descriptive terms used to define the conformational state of the component of the assembly - for example, native, unfolded, etc. (Editable)

Molecules in Entry

Table 12
Name Name of template molecule
Molecule Type Standard derived type of molecule - for example, protein, DNA, RNA, etc.
Number of Residues Number of residues in this molecule
Sequence One letter sequence of the molecule (shows the first 25 residues for longer polymers)
Is it Paramagnetic? Is this molecule paramagnetic? - derived boolean value
Database Name Database name of cross reference (for example UniProt, GenBank, PDB, etc.), setting this will set a temporary value for the accession code, which should be set to the correct value (Editable)
Database Acc. Number Accession number for cross reference - it can only be set after adding a database name and will then be initialised to ‘TmpAcc’ (Editable)
Database Details Additional details pertaining to the database cross reference (Editable)
Domain or Fragment Give the name of the fragment if the protein or necleic acid is a part of a larger molecule with a well established biological function (Editable)
EC Number Enzyme Commission number if the molecule is an enzyme (Editable)
Mutations Specify any mutations that have been introduced into the molecular entity - for example, Y20A (Editable)
Details Additional details pertaining to this molecule or its sequence (Editable)

Non-standard & Non-polymer Chem Comps

Table 13
CcpCode The CCPN code of the compound
PDB Code The PDB three-letter code of the compound
Mol. Type Derived molecule type of chemical component - for example, protein, ???
Name The long chemical name of the compound

Sources

Add experimental and biological sources

Experimental Sample Sources

Table 14
Scientific Name The standard scientific name for the source organism of this molecule - choose from a list of standard recombinant organisms or ‘synthetic’ (Editable)
Common Name The common name for the source organism of this molecule (Editable)
Molecule The name of the linked template polymeric molecule
Production Method The method that was used to produce the organism - choose from a list including recombinant technology, chemical synthesis, etc. (Editable)
Host strain Strain information about the source organism (Editable)
Vector Type The type of vector used such as plasmid, cosmid, etc. (Editable)
Vector Name The specific name of the vector used if applicable (Editable)
Cell Line The cell line that was used if applicable (Editable)
Variant Variant details about the source organism if applicable (Editable)
Details Additional details about the production method or source organism (Editable)

button Add Polymer Experimental Sources: Adds experimental and natural sources for all polymers in the molecular system

button Remove Experimental Source: Remove the currently selected experimental source

Biological & Sequence Origin

Table 15
Scientific Name The standard scientific name for the biological or natural source of this molecule - choose from a list of the most common organisms in the PDB, which will also set the common name (Editable)
Common Name The common name for the biological or natural source organism of this molecule (Editable)
Molecule The name of the linked template polymeric molecule
Organism Type The type of organism that the molecule is from - for example, organism, virus, plasmid, no natural source, etc. (Editable)
Strain Strain information about the source organism (Editable)
Variant Variant details about the source organism if applicable (Editable)
Gene Name Name of the gene that the protein is produced from (Editable)
Cell Line The cell line that the protein is made from if applicable (Editable)
ATCC Number American Type Culture Collection number if sample comes from that organisation (Editable)
Organ The organ in which the protein is located if applicable (Editable)
Tissue The tissue in which the protein is located if applicable (Editable)
Cell Type The cell type that the protein is made from if applicable (Editable)
Organelle The organelle in which the protein is located if applicable (Editable)
Details Additional details about the host biological organism (Editable)

button Add Polymer Natural Sources: Adds natural sources for all polymers in the molecular system (these are usually added when experimental sources are added)

button Remove Natural Source: Remoevs the currently selected natural source

Samples

Add sample, sample component and isotope labelling information

Samples

Table 16
# The serial number of the sample
Name The name used to label the sample
Solvent System The solvent composition of this sample - for example, 90% H2O/10% D2O, 100% D2O, etc. (Editable)
Details Additional details about the sample (Editable)

button Add Sample: Add a new sample to the CCPN project

button Remove Sample: Remove the currently selected sample from the CCPN project

Sample Components

Table 17
Molecular Component Common molecular name of the component from the sample selected in the top frame
Isotopic Labelling Isotopic labelling in standard IUPAC format - a common set is given in the pulldown menu or use the example provided to specify your own isotopic labelling (Editable)
Concentration Concentration value (Editable)
Error Error in concentration value (Editable)
Unit Unit of concentration - from: ‘kg/m3’, ‘M’, ‘m3/m3’, ‘mol/mol’, ‘kg/kg’ - use ‘m3/m3’ to solute ratios (Editable)

button Add Polymer Sample Components: Add the names of all polymeric components from your molecular system

button Add Other Sample Component: Add the names of other components in this sample

button Remove Sample Component: Remove the currently selected component

NMR Conditions

Add experimental conditions used in your NMR experiments

NMR Condition Sets

Table 18
# The serial number of the condition set
Condition Set The name used to label the condition set (Editable)
Details Additional details about the condition set (Editable)

button Add Condition Set: Add a new condition set to the CCPN project

button Remove Condition Set: Remove the currently select condition set from the CCPN project

NMR Conditions

Table 19
Condition The name of the variable used to define a specific sample condition - for example, temperature, pH, etc.
Value The experimental value of the condition selected (Editable)
Error The experiemental error in the condition selected (Editable)
Unit The unit used to measure the condition - for example, K for temperature (Editable)

button Add Standard Conditions: This button adds the four standard condtions: temperature, pH, pressure and ionic strength

button Add Condition: Add other types of condition to the set

button Remove Condition: Remove currently selected condition from the set

Instruments

Add NMR spectrometers and probes

NMR Spectrometers

Table 20
# Serial number of the NMR spectrometer specification
Name A name for the spectrometer, for graphical displays (Editable)
Nominal Freq. The rounded spectrometer frequency, from the 1H resonance frequency in MHz, used in textual description - for example. ‘500’, ‘900’
Proton Freq. (MHz) The actual numeric magnetic field strength expressed as a 1H resonance frequency in MHz (also sets and rounds the nominal value) - for example ‘500.013’ (Editable)
Manufacturer Manufacturer name - choose from a list including Bruker, Varian, GEOL, Custom, etc. (Editable)
Model The manufacturer’s definition of the spectrometer model - choose from a list based on the manufacturer (Editable)
Serial # The manufacturer’s serial number for the specific NMR spectrometer (Editable)
Details A user-specified textual comment about the NMR spectrometer (Editable)

button Add Spectrometer: Add a new NMR spectrometer specification to the CCPN project

button Remove Spectrometer: Delete the selected NMR spectrometer specification from the CCPN project

NMR Probes

Table 21
# Serial number of NMR probe specification
Name The name of the probe for graphical representation (Editable)
Type A classification for the kind of probe used - for example, liquid, solid, nano, flow or MAS (Editable)
Manufacturer Manufacturer name (Editable)
Model The manufacturer’s definition of the probe model (Editable)
Serial # The manufacturer’s serial number for the specific NMR probe (Editable)
Diameter (cm) The probe diameter in cm (Editable)
Details A user-specified textual comment about the probe (Editable)

button Add Probe: Add a new NMR probe specification to the CCPN project

button Remove Probe: Remove the selected NMR probe specification from the CCPN project

Experiments

Add NMR experiments and link data about samples, conditions, instruments, shift references and shift lists added in the previous tabs to the experiments

Experiments

Table 22
Name The textual name for the experiment, for graphical displays (Editable)
Submit? Is this experiment to be submitted? - toggle by clicking (note if the experiment is part of a selected peak list, it will automatically be submitted) (Editable)
Systematic Name The name defined by the CCPN data model for this experiment or the user-defined name if no reference NMR experiment has been defined
Sample State The state that best describes the sample and any molecular ordering; liquid (solution), solid, powder, ordered or crystalline (Editable)
Sample Choose which sample was used to perform the experiment from the list added to the CCPN project in the “Samples” tab (Editable)
Condition Set Choose which sample condition set was used to perform the experiment from the list added to the CCPN project in the “NMR Conditions” tab (Editable)
Chemical Shift Ref. Choose multiple chemical shift references were used for any chemical shift list that the experiment was used to compile from the list added to the CCPN project in the “Shifts” tab (Editable)
Raw data? Is the raw data available?
Spectrometer Choose which NMR spectrometer was used to perform the experiment from the list added to the CCPN project in the “Instruments” tab (Editable)
Probe Choose which NMR probe was used to perform the experiment from the list added to the CCPN project in the “Instruments” tab (Editable)
Chemical Shift List Choose a chemical shift list that the NMR experiment was used to compile, if applicable - the shift list should be selected for submission in the “NMR Data” tab (Editable)

button Add Experiment: Add a new NMR experiment record to the CCPN project

button Remove Experiment: Remove the currently selected NMR experiment from the CCPN project

button Submit All: Add all NMR experiments in the list to the “Entry” deposition object

button Submit Minimal: Just submit a minimal list of NMR experiments - any experiments used in submitted peak lists will remain to be submitted

Structures

Add a structure generation and link a structural ensemble and restraint sets to it

Structure Generations

Table 23
Structure Generation # The serial number of the structure generation
Name The name used to label the structure generation (Editable)
Submit? Is this structure generation to be submitted? - toggle by clicking (Editable)
Generation Type Type of structure generation - denovo or refinement (Editable)
Details Additional details about the structure generation (Editable)
Software Software used to make the structure ensemble in this structure generation - the software will also need a method selected in the “References” tab (Editable)
Ensemble # Select from the structure ensembles in the CCPN project (shown in the middle frame) that was calculated using this structure generation (Editable)
Constraint Set # Select from the constraint sets in the CCPN project (shown in the bottom frame) that was used to calculate the structure ensemble in this structure generation (Editable)

button Add Structure Generation: Add a new structure generation to the CCPN project

button Remove Structure Generation: Remove the currently selected structure generation from the CCPN project

Structure Ensembles

Table 24
Structure Ensemble # The serial number of the structure ensemble
Details Additional details about this structure ensemble (Editable)
Models Number of models selected in this structure ensemble
Chains A list of chains in the molecular system that are represented in the structure ensemble
Residues The number of residues summed over all chains represented in the structure ensemble
Calculated Models Number of models calculated in this structure ensemble (Editable)
Selection Criteria Criteria used to select models to represent the structure ensemble from all calculated models (Editable)
Representative Model The representative model for the structure ensemble (Editable)
Selection Criteria for Representative Criteria used to select the representative model in the structure ensemble (Editable)

Constraint Sets

pulldown Constraint Set: Choose a constraint set from the CCPN project (there may be multiple constraint lists in each set)

Table 25
Constraint List # The serial number of the constraint list
Constraint Type The type of constraints in this list - for example, distances, NOEs, dihedral angles, RDCs, etc
Name The name used to label this constraint list (Editable)
Details Additional details about this constraint list (Editable)
Number of Constraints The number of constraints found in this list