Trimer processing workflow » History » Version 1
Dmitry Lyumkis, 06/24/2013 09:45 PM
1 | 1 | Dmitry Lyumkis | h1. Trimer processing workflow |
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3 | h1. reconstruct an ab initio model using common lines |
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5 | # select a set of ~20 good class averages, and upload them as a template stack (call it, e.g. "ts_2g12_initial_models") |
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6 | # select as many of the class averages that have reliable features which you think are real and correspond to the Fab-bound complex (could be 50, could be 100, etc …), and upload that as another template stack (call it, e.g. "ts_2g12_refinement") |
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7 | # You can access the common lines method under the menu "ab initio reconstruction" and "automated common lines" in Appion. Go there. |
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8 | # Under "iterative model creation" select the first template stack, "ts_2g12_initial_models" |
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9 | # Under "refinement of aligned and clustered model" select the second template stack, "ts_2g12_refinement" |
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10 | # keep all parameters as default, and use EMAN for iterative model creation. Then fill out the number of images per volume. This should be ~50% of the number of images in the "ts_2g12_initial_models" stack. If you have, e.g. 30 images, this value should be ~15. |
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11 | # Fill out the bottom radii for the particles and give a mass. For example, for 2g12, these should probably be: radius of mask=200 ; inner alignment radius = 0 ; outer alignment radius = 140 ; particle mass = 750 |
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13 | # Launch the job on guppy (you can also try garibaldi, but I know that guppy works) |
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14 | # repeat 1-8 with an identical job, EXCEPT that uncheck "iteratively align class averages to each other", AND give the run a different name (for example, you can have two runs, titled "acl1" and "acl1_noiteralign" …). |