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Comparing Structures

1) The document provides instructions for comparing hemoglobin structures using the Chimera software, including how to open specific hemoglobin structures from the PDB database, color different parts for visualization, and overlay the structures for structural comparison. 2) Key steps include opening the 1HHO and 2HHB hemoglobin structures from the PDB, deleting solvent and other artifacts, using the model panel to control visibility of structures, and coloring different parts like the F helix or heme group. 3) Structures can then be overlaid using the "Matchmaker" tool to highlight configurational differences between oxyhemoglobin and deoxyhemoglobin.

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31 views

Comparing Structures

1) The document provides instructions for comparing hemoglobin structures using the Chimera software, including how to open specific hemoglobin structures from the PDB database, color different parts for visualization, and overlay the structures for structural comparison. 2) Key steps include opening the 1HHO and 2HHB hemoglobin structures from the PDB, deleting solvent and other artifacts, using the model panel to control visibility of structures, and coloring different parts like the F helix or heme group. 3) Structures can then be overlaid using the "Matchmaker" tool to highlight configurational differences between oxyhemoglobin and deoxyhemoglobin.

Uploaded by

megsmama
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Instructions for how to use Chimera to Compare Structures (details for viewing hemoglobin structures are in blue) To fetch

a structure from the command line: Open Chimera Favorites/Command line In the command line, type: Open #xxx where #xxx is the 4 character pdb id code. The pdb codes for human hemoglobin are: 1HHO = human oxyhemoglobin 2HHB = human deoxyhemoglobin You can delete solvent, zinc, and phosphate to make viewing easier. For the solvent, type: del solvent To specify a specific residue/molecule, use the residue name that is in the pdb file. In this case zinc is zn and phosphate is po4. Specify a residue by using a colon before the residue name. For example, del :zn will delete the zinc atoms in the structure (these are there as an artifact of the crystallization solution). Another useful dialog box is the model panel: Favorites/Model Panel The model panel will show- and allow you to control- all molecules that are displayed on the screen. Each structure that you open is given a number; the first one is number 0, the second is 1, etc. These numbers can be used on the command line, preceded by the # sign. For example, if you imported 1hho first, then it would be model #0. The A and the S check boxes let you move the models independently (A= active, so whichever model is active will respond to mouse movements) or to hide one of the models (S=show, so if this is unchecked, the molecule is hidden). If you wanted to be able to distinguish between two models by, say, coloring them different colors, you could use the color command followed by the desired color, then molecule (or residue, or atom, etc.) specifier. To color the oxyhemoglobin molecule red, you would type: color red #0

Lets say youd like to look at the F helix, which spans residues 118-138, you could color it green with the command: color green #0:118-138 (the spaces are important between the keywords, but there should be no spaces in the atom specification- the #0:118-138 part) color white :hem color white #0:hem color brown #0:hem@fe The first of these commands colors the heme in both models white, the second colors only the heme in model #0 white, and the third would color the iron coordinated to the heme in model #0 brown (the @ sign is the specifier for a particular atom-you get the idea). How to compare structures in Chimera Once you have your models colored so that you can distinguish the two models, or parts of them, in the way you want, you can overlay the models to align the molecules as closely as possible. This will allow you to highlight configurational differences between the two states of hemoglobin (or whatever your molecule of interest is). To do this: Tools/Structure Comparison/Matchmaker You will need to select one of the structures as a reference structure and the other as a structure to match. Click apply, then OK to exit. Voila! You have aligned two protein structures and can now move them about and zoom in and out to examine structural details. One final note: Remember, if you want to know the atom or residue designation for a particular portion of your structure, look it up in the pdb file text, which can be viewed online at the pdb database (www.rcsb.org).

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