Appion

h1. Particle Selection

The first step in single particle analysis is to pick the particles within the micrographs. Basically three main ways exist to do this, all of them are integrated within Appion. Based on the shape of the particle, the prior knowledge and the amount of data collected, the user has to make a decision which approach is the best or use different approaches simultaneously and see which works best.

h2. 1. [[Manual Picking]]

The manual particle picker allows the user to select the targets by eye. This can be extremely time consuming. However, if no starting model is available or the desired particles are represented in a very low concentration it is sometimes worth to spent some time selecting the particles manually. After several hundred particles have been collected a preliminary initial model or 2D averages can be generated and used as templates.

h2. 2. [[Template Picking]]

Template picking is usually the most accurate and convenient way to extract particles. Once an initial model or 2D averages have been acquired they can be used as templates to identify similar particles within the micrograph.

h2. 3. [[Dog Picking]]

Use Dog Picker if you have no accurate idea of what your particle looks like or you simply want to pick everything (this will include blobs of noise). 

h2. 4. Random Conical Tilt Picking

If you ran a random conical tilt session you have to pick and correlate the particles on the tilt pairs.

To find the particles you can use [[Template Picking]], [[Manual Picking]] or [[Dog Picking]]. To correlate the picks use one of the following options.

h3. [[Align and Edit Tilt Pairs]]

manual align and editing of the tilt pairs

h3. [[Auto Align Tilt Pairs]]

automated align and editing of the tilt pairs

!http://emg.nysbc.org/attachments/277/Picture_81.png!

h2. 5. [[Repeat from other Session]]

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[[Processing Cluster Login|< Processing Cluster Login]] | [[CTF Estimation|CTF Estimation >]]

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