AutoDep Notes for First Time Users

This is a description of how to submit data to the PDB at PDBe. AutoDep guides you through the process of completing your submission.

How to Begin Your Submission

• The deposition can be based on a previously completed or part-completed deposition
• The deposition can be based on a publicly released PDB entry
• The deposition can be based on a completed internal deposition
• A new deposition can also be started from scratch

If the new deposition is based on a previously completed deposition, a publicly released PDB entry or an internally deposited entry then AutoDep merges the relevant data from these sources, and this information is displayed in the relevant sections in AutoDep. Please make sure that you delete the information which is not applicable to your entry.

Every deposition is partially verified as you add new information.

The entry is checked by AutoDep processing programs and the PDBe returns this report via AutoDep for your information. An effort is made to provide all the relevant links that may be useful in constructing your submission.

Overview of the Process

Security and Confidentiality: We provide you with a deposition number consisting of three letters, a dash, and a number, and ask you to provide a password. Anyone who knows both the deposition number and the password has access to your submission. This allows you to make future submissions based on earlier ones. If you prefer us to block all access at the completion of the deposition process, please instruct us accordingly. This may be done in the section entitled Instructions to the PDBe.

You may change your password at any time by choosing Change Password in the Control Panel.

The first 5 sections are mandatory and have to be completed and a coordinate file has to be uploaded in order to proceed with the deposition. The mandatory sections consist of:

• Initialisation
• Instructions to AutoDep
• Title & Author
• References
• Software

Initialisation:

The first section requires you to select the primary experimental technique used for determining the structure which is being deposited. Changing the experiment type once selected will remove all uploaded files and reset the data. This section also requires information about contact author. The contact author has authority to grant approval for release of the completed PDB entry. The review copy of the PDB entry, validation diagnostics, and approval request will be sent to the contact author. The contact author should be able to help in preparing the entry if we need any answers or clarification.

Instructions to AutoDep:

Once you complete the Initialisation information you are asked about specific processing details, data release or hold requests, and whether this data set replaces an existing released entry.

The PDBe does not allow you to request a specific PDB_ID_CODE.

Title & Author:

Once you complete the 'Instructions to Autodep' information you are asked about the title and authors for this entry. The title is free text and describes the contents of the entry and procedures or conditions which set this entry apart from others. The title presents an opportunity for the depositor to emphasize the underlying purpose of this particular experiment. Entries consisting of only alpha carbon atoms should state this in the title.Keywords relevant to the structural entry is also requested.

References:

Once you complete the 'Title and Author' information you are asked to cite both the primary reference which identifies the deposited set of coordinates as well as other important references. If you have chosen to release your data upon publication, you must notify the PDBe as soon as your paper is published.

Software:

Once you complete the 'References' information you are asked to select the refinement program used. Programs such as CCP4, CNS, SHELXL-97, X-PLOR can output the refinement statistics in HARVEST FILES or as PDB format. You may MERGE these into AutoDep automatically without having to enter this data by hand. See the Help Page section on Uploading and Merging Files for more details.

CHANGING THE REFINEMENT TYPE ONCE SELECTED WILL RESULT IN A LOSS OF ALL DATA IN THE NON-MANDATORY SECTIONS AND REMOVAL OF ALL FILES UPLOADED.

File Deposition:

You will need to upload your coordinates which must be in PDB format as described in the PDB Contents Guide, and structured as described in Tips on Preparing the Atomic Coordinate File, unless a CNS HARVEST file containing coordinates is uploaded. In such case coordinates will be extracted from the CNS HARVEST file.

You can upload HARVEST files from CCP4 and CNS and merge the relevant information using AutoDep and not have to enter this data by hand. The HARVEST files from programmes SCALA, TRUNCATE and REFMAC in the CCP4 suite of programmes can be uploaded as a tar file.
See the Web sites, listed on the Help Page, for CCP4, CNS program packages for details on generating HARVEST files.

Other files that you may upload include structure factors; NMR constraints, chemical shifts, or structure and constraints statistics; file(s) containing PDB header records; parameter and topology files; structure description file(s); other files such as kinemages, rasmol scripts, or images of the structure.

Programs such as SHELXL-97, X-PLOR, O, and CNS can output the refinement statistics in PDB format. Each has the means of outputting PDB files. You may MERGE these into AutoDep automatically and not have to enter this data by hand. See the Web sites, listed on the Help Page, for each of these program packages for details on generating this output.

We encourage you to send your structure factors in ASCII format. If you are using CCP4, we suggest that you run the MTZ2various routine to convert the binary file into ASCII.

Select the description of the file to be uploaded, enter its complete path and filename by typing it in the field or by using the Browse button, and click on the Upload button. Repeat these steps for every file being uploaded.

DELETING THE COORDINATE FILE WILL RESULT IN A LOSS OF ALL DATA IN THE NON-MANDATORY SECTIONS AND REMOVAL OF ALL FILES UPLOADED.

Remaining Sections:

Continue your AutoDep session by selecting the next section from the control panel. From this point on, AutoDep will jump automatically to the next unfinished section each time you successfully complete a section.

Complete the remaining sections, taking time to make the best submission possible.

After writing your values into the fields on a page, you must click on the Save button found at the bottom of every section in order to write the data to your AutoDep file at the PDBe. If you do not do this before moving on to the next section, this information will be lost.

The n/a button to the right of every non-mandatory field places the value n/a, for not applicable, into that field. The global n/a button at the bottom of every section writes n/a into every blank field of the current page. Mandatory fields expect the answer none or null to be acceptable. The example given at the right of the answer field shows the type of answer that is acceptable.

General Instructions:

Residue Identification:

Whenever you are asked to identify residues, such as in the Sequence section, residues names must be given in four (4) parts: the residue name, chain identifier, sequence number, and insertion code, using the "?" as placeholder. For example:

 GLY ? 31 ?    indicates GLY with a null chain identifier, 
	       sequence number 31, and no insertion code                 

 VAL B 235 A   refers to VAL in chain B, sequence number 235, 
               insertion code A                 
			

Insertion Codes

The insertion code is commonly used in sequence numbering. While in most cases the amino acids that comprise a protein are numbered sequentially starting with 1, there are a number of situations that may give rise to different numbering schemes:

Homologous proteins can exist in a number of different species. Depositors may use a residue numbering scheme in order to preserve the homology. The reference protein may be numbered sequentially starting with 1. When aligned to reference protein, if there is a deletion of residues in the homologous sequence, residue numbers may be skipped so that alignment can be preserved. In case of insertion of residues in the homologous sequence relative to the reference protein, the residue numbers can be given using insertion code. Negative numbers and zeros are permitted if they are needed to align the N-terminus.

eg. (DELETION OF RESIDUES IN THE HOMOLOGOUS SEQUENCE):

REFERENCE PROTEIN NUMBERING        HOMOLOGOUS PROTEIN NUMBERING        
---------------------------------------------------------------------
            59                                  59                      
            60                                  60                      
            61                                                          
            62                                  62    
                  
eg. (INSERTION OF RESIDUES IN THE HOMOLOGOUS SEQUENCE):

REFERENCE PROTEIN NUMBERING         HOMOLOGOUS PROTEIN NUMBERING        
---------------------------------------------------------------------
            85                                  85                      
            86                                  86                      
                                                86A                     
                                                86B                     
            87                                  87                      

			

The numbering of a proenzyme may be used for the enzyme following cleavage.

The molecule studied might be a portion of the whole protein. The residue numbering scheme could show the relationship to the intact protein.

The protein might be a mutant with residues inserted or deleted. As above, the residue numbering of the native protein could be preserved by appropriate use of gaps in the numbering and/or insertion codes.

Atom Name:

Atom names must be given in two (2) parts: the atom name and its alternate location indicator. A question mark (?) must be used as placeholder if the alternate location indicator is null.

For example:
CA ?    refers to CA with no alternate locations
N ?     refers to N with no alternate locations
CG1 A   refers to CG1's first position, alternate location A
CG1 B   refers to CG1's second position, alternate location B
			

If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator.

You may preview the PDB file at the end of submission process by clicking on the Preview PDB Header button.

You may view your coordinates any time after they have been successfully uploaded by clicking on the Coordinates File button.

Release Protocol

The PDB ID code will be issued only after you do the following:

Answer all mandatory questions

You can recognize these within AutoDep as those questions that do not have the n/a button after the field. If the field is not appropriate for your data, you must answer NONE or NULL as indicated in the example following the answer field. An n/a will not be accepted in these mandatory fields.

Some verification is done at the time you Save for each page. Carefully note any returned remarks. Double-check the entered data. If it is correct, just hit Save again and the data will be accepted for validation. If necessary, replace with the correct data and Save.

Pass the minimum validation criteria

Once all sections are complete, click on the Validate link which will appear in the control panel. This will initiate the validation procedure which could take from 10seconds to 20 minutes. You will be notified via email when the validation procedure is complete. When you recieve this email indicating that validation is complete, then please re-login to the entry or reload the page. A new Reports section will appear in the control panel.

You should carefully review the output report. Once you have viewed your reports click on the Reports link again in the control panel or click on the links at the top/bottom of the reports page. If you are happy with the report then accept the report by selecting 'yes' and save or select 'no' if you choose to correct and resubmit your data.

You will then be requested to submit the deposition.

Approve the immediate release of your data

All entries are further annotated at the PDBe and returned to the depositor for review. Upon receipt of approval or in the case of entries flagged as immediate release, if no reply is received from the depositor the annotated entry will be released after 3 weeks from the date of deposition. If you have placed your coordinates on hold, the data will be released on the hold-release date.

Following submission, PDBe staff will process the entry. This processing will include standardization of nomenclature, data representation, and other annotation. Heterogens and Special Processing Instructions provided by the author will be addressed during this time.

The PDBe will release final files to the Research Collaboratory for Structural Bioinformatics (RCSB) within three weeks of their receipt or at the time of their removal from Hold Status.

Updates will be loaded onto the PDBe server once a week.