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[Frequently Asked Questions]

1. Update & download of PDB data

2. Various Search services at PDBj

3. Usage Policies & Privacy Policies

4. Software and services provided by PDBj

5. Other inquiries

6. Troubleshooting

7. Deposition, update and release of PDB entries

Please also refer to wwPDB FAQ page. Regarding wwPDB New Deposition and Annotation system, refer to wwPDB FAQ page about new system.


2-1) Is there a tutorial available on how to use various search services at PDBj?

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4-2) jV: Do you have a tutorial on the 3D viewer, jV?

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4-3) jV: What are the system requirements, e.g. operating system, to use jV?

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4-4) jV: How do I change the background color?

A) When you change the background color, use the command set.
The following example will change the background color to blue.

set background blue
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4-5) jV: How can I display a certain amino acid and/or atoms, in addition to the entire structure in ribbon model?

A) The structure is displayed in ribbon model when you select [Cartoon] from jV [Display] menu.
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To display a certain amino acid or atom in spacefill model, select the target with the select command first, and then select [Spacefill] from the [Display] menu.

example 1) Selecting by residue number:
select 32 || 64
  
example 2) Selecting by a combination of residue number and atom name:
select 32 && (ASP.OD1 || ASP.CG || ASP.OD2)
  

For more details on atom expressions, please refer to the Atom Expressionpage

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4-6) jV: How do I save a jV image?

A) To save the jV image as a PNG/JPEG file, click on [File] > [Save] > [PNG/JPEG] and choose a folder to save the file to.
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You can also use the command, save, as an alternative in using the stand-alone jV.

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4-7) jV: How can I save a higher resolution image?

A) You can save a higher resolution image by enlarging the jV window within the screen.

Use a command set to enlarge the jV window in specified pixels as shown below:

set imagesize 800 800
  

Also, to magnify the protein image, use the command zoom. The number is specified as a percentage.

zoom 130
  

After that, save the image by clicking on [File] > [Save] > [(file format)].

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4-8) EM: I have a question about EM Navigator. Who do I contact?

A) Please see the FAQ page of EM Navigator. If you do not find the answer to your question, please feel free to contact us.

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4-9) EM: How do I reproduce a map from a session file of EM Navigator?

A) Please download a session file and a map file from EM Navigator's Detail page. Please put the decompressed map file and the session file in the same directory. Restore the session using UCSF Chimera and the atomic model and the map will be displayed. The fitted model of the atomic model and the map surface can also be viewed using Yorodumi.

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4-10) GIRAF: I submitted a query by uploading PDB file but I got result page with no result.

A) The GIRAF service requires atom symbols described in 77 and 78 columns of each ATOM records. Some applications output PDB format files without atom symbols and GIRAF can't process these data correctly. Please add them and submit again.

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5-2) Do you have a reference regarding PDB XML format and various services?

A) Please refer to the following reference on XML format.

PDBML: The representation of archival macromolecular structure data in XML
Westbrook, J.D., Ito, N., Nakamura, H., Henrick, K., Berman, H.M.
Bioinformatics 21 (7): 98 (2005) [PubMed] [doi:10.1093/bioinformatics/bti082]

Other publications are listed on the Publication page.

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A) The XML Schema files for PDBML and PDBMLplus data are available on the following pages:

PDBML:
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PDBMLplus:
PDBMLplus schema page

See PDBj Help page for the details of the data format, PDBML and PDBMLplus.

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5-4) How do I link to a Structure Summary page of PDBj Mine for a PDB ID?

A) The correct syntax for linking to a Structure Summary page for a structure by PDB ID on the site is as follows (example 1NIH):

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5-5) Why is "j" written in lowercase while "J" of Japan is written in uppercase?

A) PDBj ( P rotein D ata B ank J apan) maintains a centralized PDB archive of macromolecular structures as a member of the wwPDB collaborating with the RCSB, the BMRB in USA and the PDBe in EU.

To emphasize PDB which is written in uppercase, we write a site identification character, the last j, in lowercase.

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5-6) How can I uncompress gz file(.gz) on Windows? How can I compress a file into gz format on Windows?

A) Windows supports ZIP(.zip) as a standard compression/uncompression format. Please download a compression/uncompression software to use gzip or other compression format.

The following are examples of free softwares.

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6-1) I cannot access to your ftp site using the IP address these days. I used to do that.

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PDBj FTP Server (incl. PDB Archive): ftp.pdbj.org
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6-2) jV: RasMac does not recognize PDB files.

A) It is possible that RasMac has a bug on recognizing data format.
To avoid this problem, change the extension of the file from .pdb to .txt or relate the .pdb file to RasMac.

You can use jV, an interactive 3D viewer program to visualize protein and nucleic acid molecules, which has been developed and updated by PDBj. Please see Installation of jV3 page.

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6-3) jV: I have a problem displaying a PDB structure using PDBjViewer. What can I do?

A) PDBj Viewer is the old version of jV. Please install the latest version of jV.

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6-4) jV: I encounter an error when using jV applet to view a structure.

A) When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux, jV applet and applet-launcher fails to start up with the following error.

Error:java.io.IOException:Cannot find certificates for JNLP
 AppletLauncher class

Please use JRE6 Update17 (1.6.0_17) or later.

If you have any other viewing problems, please refer to the jV wiki Trouble shooting page.

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6-5) jV: I have a problem in installing jV and/or displaying a PDB structure using jV.

A) If you have installation or viewing problems, please refer to the jV wiki Trouble shooting page.

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7-1) Do you have documentation for the PDB file format?

A) Documentation describing the PDB file format and annotation policies is available from the wwPDB at http://www.wwpdb.org/docs.html.
Please refer to the newest version of thePDB file format - Contents Guide.

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7-2) I want to change my PDB entry but do not know the contact e-mail address. What can I do?

A) Please contact the PDBj deposition and annotation staff using this form.
Be sure to include the PDB ID or RCSB ID in the subject.

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7-3) Can I complete a deposition over a few days? For how long is my incomplete deposition session saved?

A) Yes, you can complete depositing a structure using wwPDB deposition system over a few days.
In fact, your incomplete session is saved for a limit of 6 months from when it is first started.

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7-4) When will an HPUB structure be released? The primary citation has been published.

A) We would appreciate it if you could provide the publication information from the Contact Us page.
The structure will be released the next Wednesday at 9 a.m.(JST) at the earliest, otherwise, on the Wednesday of the following week.

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7-6) What is the rule for assigning chain IDs? How are upper case letters, lower case letters and numbers used?

A) Please refer to 4 Chain ID assignment of Processing Procedures manual at http://www.wwpdb.org/docs.html.

Upper case letters and numbers should be used first for chain IDs. Lower case letters should be used only after all upper letters and numbers 0-9 have been used. In this way, a maximum of 62 chains can be included in the PDB entry. Other symbols should never be used for chain IDs.

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7-7) Can I release my PDB entry (deposited as HPUB/HOLD) right away?

A) PDB entries can always be released at depositors request once annotation is complete .

Please contact the PDBj deposition and annotation staff using this form.
Be sure to include the PDB ID or RCSB ID in the subject.

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Created: 2020-11-02 (last edited: more than 1 year ago)2020-11-02

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數據於2024-03-13公開中

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