Retrieving and working with PDB information

This is a step by step rundown intended to give you an idea of how to work with Molecular Origami.
The pages page links to pages which are best viewed in windows with a 800x600 display area.
It may be convenient to print this page and work off a paper copy.

Open Molecular Origami

On the main screen

  • Select - Search Brookhaven Protein Data Bank NOW to open the search screen.

    On the search screen

  • Enter hemoglobin in the compound box.
  • Click Send Request to start the search.
  • Click OK when the search is done.
  • A list will come back of 86 Matching ID Codes.
  • Highlight the protein 1ash and click - Fetch the Entry with ID Codes:
  • This will make a .pdb file and open Molecular Origami.

    In Molecular Origami

  • Highlight HEM 301 in the PDB data box
  • Click Add Selected
  • Rotate the picture with the mouse (the two mouse buttons are different)
  • Zoom in with the vertical scroll bar
  • Right click on the orange Fe in the center
  • Choose Move Center Atom to .HEM..301_FE from pop up menu
  • Then choose Append All Groups Within 300 pm of __
  • Right click on the number 1 and enter a name to save the view
  • Now the screen should similar to this
  • In the lower right hand corner click on the MO...

    In the Design Studio

  • Lower the scale to 150 to make it easier to see
  • Rearrange to get as small as possible
  • Make sure you do not have faces that overlap
  • If you can, enlarge the scale to 200 (It is possible).
  • Select Print
  • Click on the red underlined printer
  • Change it to an acceptable printer.
  • Print by clicking OK
  • Exit the design studio by choosing File - OK.

    Play around

  • Save a few different views
  • Try lengthening to the amino acid chain
  • Take a look at the text file by clicking text...
  • If you have it, view the protein with Rasmol...
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