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picker:tilt_pair_picking [2017/06/12 15:22] kbertra2 |
picker:tilt_pair_picking [2017/06/12 19:40] kbertra2 |
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| - If working with more than one set of tilted pair files of the same sample, you may want to combine your data. To do so, find the [[eyes:logics:Append|]] logic and drag it into your workspace. Connect this logic with your imported data. Continue this process until all of your data for untilted or tilted particles is combined into a single [[eyes:logics:Append|]] logic (i.e. at the end you should have two [[eyes:logics:Append|]] logics; one for tilted data and one for untilted data). At this point, your logics should be connected as shown by the following: {{ :picker:selection_006.png |}} | - If working with more than one set of tilted pair files of the same sample, you may want to combine your data. To do so, find the [[eyes:logics:Append|]] logic and drag it into your workspace. Connect this logic with your imported data. Continue this process until all of your data for untilted or tilted particles is combined into a single [[eyes:logics:Append|]] logic (i.e. at the end you should have two [[eyes:logics:Append|]] logics; one for tilted data and one for untilted data). At this point, your logics should be connected as shown by the following: {{ :picker:selection_006.png |}} | ||
| - | == Tilted Data == | + | **Tilted Data** |
| - From this point, work with //tilted data// until otherwise noted. You will deal with the tilted and untilted data separately. Once the data is appended, it needs to be filtered. Find the [[eyes:logics:Filtering|]] logic and connect it with the [[eyes:logics:Append|]] logic. Click on the [[eyes:logics:Filtering|]] logic and apply the following settings: Processor = Gauss bandpass, Upper frequency = 0.6, Lower frequency = 0.04, Show filter function = unchecked, Transmission = 0. Click the "Play" icon to run the logic. | - From this point, work with //tilted data// until otherwise noted. You will deal with the tilted and untilted data separately. Once the data is appended, it needs to be filtered. Find the [[eyes:logics:Filtering|]] logic and connect it with the [[eyes:logics:Append|]] logic. Click on the [[eyes:logics:Filtering|]] logic and apply the following settings: Processor = Gauss bandpass, Upper frequency = 0.6, Lower frequency = 0.04, Show filter function = unchecked, Transmission = 0. Click the "Play" icon to run the logic. | ||
| - Next select the [[eyes:logics:Normalization|]] logic and connect it to the [[eyes:logics:Filtering|]] logic of the previous step. Click on the [[eyes:logics:Normalization|]] logic and apply the following settings: Processor = Normalize against background, Invert = (select yes if micrographs were acquired in negative stain). | - Next select the [[eyes:logics:Normalization|]] logic and connect it to the [[eyes:logics:Filtering|]] logic of the previous step. Click on the [[eyes:logics:Normalization|]] logic and apply the following settings: Processor = Normalize against background, Invert = (select yes if micrographs were acquired in negative stain). | ||
| - | - Find the [[eyes:logics:Rct2|]] (random conical tilt) logic and connect it to the output of [[eyes:logics:Normalization|]] to "io:tilted" input of the [[eyes:logics:Rct2|]] logic. Before running the [[eyes:logics:Rct2|]] logic, click on it and adjust the settings as shown below (note: pixel size varies): | + | - Find the [[eyes:logics:rct|]] (random conical tilt) logic and connect the output of [[eyes:logics:Normalization|]] to "io:tilted" input of the [[eyes:logics:rct|]] logic. Before running the [[eyes:logics:rct|]] logic, click on it and adjust the settings as shown below (note: pixel size varies): |
| {{ :picker:selection_008.png |}} At this point, your logics should be set up in the following way: {{ :picker:selection_009.png |}} | {{ :picker:selection_008.png |}} At this point, your logics should be set up in the following way: {{ :picker:selection_009.png |}} | ||
| Note that the input labeled "io:untilted" has not been connected. Your //untilted// data must now be processed. | Note that the input labeled "io:untilted" has not been connected. Your //untilted// data must now be processed. | ||
| - | == Untilted Data == | + | **Untilted Data** |
| - Repeat steps 1-2 from the instructions for Tilted Data. | - Repeat steps 1-2 from the instructions for Tilted Data. | ||
| - Perform 2D operations as listed in the [[:tutorial|]]. Once you have a 2D classification, connect the "output" of your [[eyes:logics:Classification|]] to the "io:untilted" input of the [[eyes:logics:Rct2|]] logic. Click the "Play" icon to run the logic. | - Perform 2D operations as listed in the [[:tutorial|]]. Once you have a 2D classification, connect the "output" of your [[eyes:logics:Classification|]] to the "io:untilted" input of the [[eyes:logics:Rct2|]] logic. Click the "Play" icon to run the logic. | ||