PDB to Model » History » Version 2
Anke Mulder, 07/08/2010 05:39 PM
| 1 | 1 | Pick-Wei Lau | h1. PDB to Model |
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| 3 | The user is able to retrieve pdb models from the Protein Data Bank and generate a 3D density volume from the atomic model. |
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| 5 | 2 | Anke Mulder | h2. General Workflow: |
| 6 | 1 | Pick-Wei Lau | |
| 7 | 2 | Anke Mulder | *To launch:* |
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| 9 | 1 | Pick-Wei Lau | # The user enters the PDB ID (and check on the "use biological unit" check box if desired) |
| 10 | # The user decides the resolution of the density model (typically filter to 15 - 25 Angstrom resolution) |
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| 11 | # The user selects the symmetry of the model |
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| 12 | # The user selects the pixel size for the model |
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| 13 | # The user selects the box size. Note: the user needs to make sure that the box size is sufficiently large to accommodate the 3D volume to be generated. |
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| 15 | 2 | Anke Mulder | *Output:* |
| 16 | 1 | Pick-Wei Lau | |
| 17 | # Once the model is generated, it will be deposited under "3d Density Volumes" |
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| 18 | # The user then assess the quality of the model and decides whether to convert the volume into an initial model |
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| 19 | 2 | Anke Mulder | |
| 20 | h2. Notes, Comments, and Suggestions: |