Metalloprotein Site Database and Browser - FAQ

This FAQ is maintained by the team working in the development of the Metalloprotein site Database and Browser (MDB), as part of the Program Project of the Metalloprotein Structure and Design Group at The Scripps Research Institute.

If you would like to contribute to the FAQ, e-mail Jesus (jesusmc@scripps.edu). All contributors will be listed at the bottom of the FAQ

Index

1. What is the Metalloprotein Site Database and Browser?
2. What URL(s) should I use to access the MDB browser? [+]
3. How do I reference the MDB? [+]
4. Why are the bond colors not always right?
5. Why are there picking points in the middle of the bond?
6. Why is the query page so slow to load?
7. How do I get help on the functions of the MDB browser?
8. How do I navigate to other pages?
9. Is there any other way of accessing the data in the MDB?
10. How can I see the source code of the scripts you are using? [*]
11. I found a bug and/or have a comment. What should I do? [+]
12. Contributions and acknowledgments

1. What is the Metalloprotein Site Database and Browser?
   
   The Metalloprotein site Database and Browser, is the first step towards developing a distributed enviroment for interactive metalloprotein design. It is designed to provide the basic data and tools for geometrical and functional query of existing metal containing sites. It will allow quantitative analysis of the data and will be based on the current Protein Data Bank release, as well as in-house structures (TSRI). Automated tools for computational recognition of metal sites and its characteristics, will assure that the MDB will be always up-to-date.
   This is the first release of the MDB and contains 32 manually edited metal sites, as well as an automatically generated database encompasing the full PDB distribution.
   
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2. What URL(s) should I use to access the browser? [+]
   
   The best way will be using the URL for the main page of the MDB site, because it will contain the latest information on the status of the browser: http://metallo.scripps.edu/ You could also use one of the following URLs:
   
   • Current version: http://metallo.scripps.edu/current/raw.html
   • Previous version: http://metallo.scripps.edu/old/raw.html
   • The version in progress (may be unstable): http://metallo.scripps.edu/test/raw.html
   • The MDB FAQ (this document): http://metallo.scripps.edu/mdb_main/faq_mdb.html
   
   
   Back to the Index
   
   
3. How do I reference the MDB? [+]

   If you want to reference the MDB in a paper, you should use the following reference:
   
   Castagnetto, J.M.; Hennessy, S.W.; Roberts, V.A.; Getzoff, E.D.; Tainer, J.A.; Pique, M.E. "MDB: the Metalloprotein Database and Browser at The Scripps Research Institute". Nucleic Acids Res. 2002, 30(1): 379-382.
   
   If it is an on-line publication, you could add links to the MDB main site (http://metallo.scripps.edu/) and the journal's page for the paper (http://nar.oupjournals.org/cgi/content/full/30/1/379), e.g.:
   
   Castagnetto, J.M.; Hennessy, S.W.; Roberts, V.A.; Getzoff, E.D.; Tainer, J.A.; Pique, M.E. "MDB: the Metalloprotein Database and Browser at The Scripps Research Institute". Nucleic Acids Res. 2002, 30(1): 379-382. [http://metallo.scripps.edu]
   
   

   If you just want to cite the main web site, use The usual way of citing on-line references for the MLA and APA styles is somewhat similar, except for minor differences. We have adopted a variation of the format suggested in Harnack and Kleppinger's article [1] as the most amenable and informative:
   
   Author/editor. "Document Title." Title of complete work (Release #). Publication/Last revision date. <Full URL> (Date of visit).
   
   So, for the main MDB site (Release 1.5) this will be:
   
   The Metalloprotein Structure and Design Group. "MDB (Main Page) - Metalloprotein site Database & Browser, TSRI." Metalloprotein site Database and Browser (MDB, Release 1.5) September 21, 2001 <http://metallo.scripps.edu/> (November 30, 2001)
   
   And when citing, for example the MDB FAQ page:
   
   The Metalloprotein Structure and Design Group. "MDB (faq_mdb.html) - Metalloprotein Site Database & Browser, TSRI" Metalloprotein site Database and Browser (MDB, Release 1.5). September 21, 2001 <http://metallo.scripps.edu/mdb_main/faq_mdb.html> (November 30, 2001)
   
   Reference:
   [1] Harnack, A. and Kleppinger, G. "Beyond the MLA Handbook: Documenting Electronic Sources on the Internet." October 29, 1997. <http://falcon.eku.edu/honors/beyond-mla/>. (July 23, 1998)
   
   

   
   
   Back to the Index
   
   
4. Why are the bond colors not always right?
   
   We are improving the 3-D "VRML" scene descriptions to reduce superfluous points and lines, and this is an interim fix.
   
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5. Why are there picking points in the middle of the bond?
   
   Due to the way we are generating the VMRL files from the PDB structures, some extra nodes are being created. This results in sometimes being able to pick phantom "atom positions" in the middle of a bond. We are working on a way to reduce to number of nodes which will have the side effect of reducing the size of the files and thus result in a faster download.
   
   Back to the Index
   
   
6. Why is the query page so slow to load?
   
   It is slow, and it is because of the way the Java applet has been designed. We are trying to create a modular applet, which is causing that the number of connections to load it to be 80-85% of the loading traffic for the page. Hopefully with some threading we will be able to at least show part of the applet while the rest loads in the background.
   
   Jesus's comment:
   I looked at the page from home, where I use a 486SX 33 MHz laptop, with only 8MB RAM, 250 MB HD, a 28.8 Kbps modem and a 9.3 inches screen, and it takes about 3-4 minutes to load the whole thing. Slow by Web standards.
   
   To minimize the load of the applet on the users system, we have included the option to move molecules by using a "transform box", i.e. you rotate/translate/zoom a bounding box instead of the actual model. The latest released version will be usually faster than the previous one, as we improve the way our applet works.
   
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7. How do I get help on the functions of the MDB browser?
   
   If at any point you need to get help on how to use a particular part of the MDB browser, you can use the graphic bar at the top (or the text navigation bar at the bottom), to get information on the topic you want. A window will pop up, which can be resized and closed. Other topics can also be accessed from this help window.
   
   Back to the Index
   
   
8. How do I navigate to other pages?
   
   You can use the top graphic bar (or the text bar at the bottom) to go back to the main MDB page, select the database to query, go to the main Metallo Group Site, to the main TSRI site or to our page of external Web resources.
   
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9. Is there any other way of accessing the data in the MDB?
   
   We will be implementing a simpler way to access the MDB, that will not need the use of frames and Java. This interface is still under construction, and at the present time is schedule for the next release of the MDB. For now, you will need a web browser capable of using frames, Javascript and Java.
   
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10. How can I see the source code of the scripts you are using? [*]
    
    You can see the source of the scripts we are using to search the MDB, by using an URL of the form:
    
    http://metallo.scripps.edu/source/path/to/script.php3
    
    For example, to see the script "/advanced/pdbsearch.php3", use:
    
    http://metallo.scripps.edu/source/advanced/pdbsearch.php3
    
    Note: The included scripts (*.php3.inc) are in the /php_inc/ directory, so you will use, for example:
    
    http://metallo.scripps.edu/source/php_inc/tables.php3.inc
    
    You are free to use part of my (ugly) code, if you use a lot of it, you should include a reference to this web site and the name of the script upon which you based yours.
    
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11. I found a bug and/or have a comment. What should I do? [+]
    
    You can use the Feeback form or
    Send us an e-mail to the address: metallodb@scripps.edu.
    
    Please make your description of the bug(s) as detailed as possible so we can reproduce and fix it. Comments/ideas/critiques are also welcomed to the aforementioned e-mail address (be nice :).
    
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12. Contributions and acknowledgments
    
    Thanks to Mike, Sean, Marieke and especially to Melanie for all the good questions and input.
    Thanks also to all our users, and in particular to those who submitted bug reports (in chronological order):
    
    
    David Spellmeyer (dspellmeyer@combichem.com)
    Don Kurtz (kurtz@bscr.uga.edu)
    Jian Li (lijian@scripps.edu)
    Rory Melenkivitz (rm002e@uhura.cc.rochester.edu)
    Jonathan Nugent (j.nugent@ucl.ac.uk)
    Dave Goodin (dbg@scripps.edu)
    
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