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
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
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).
Click on the red underlined printer
Change it to an acceptable printer.
Print by clicking OK
Exit the design studio by choosing File - OK.
- Click on an edge - a red dot appears on another edge
- Double click on an edge and it repositions at the red dot
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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