Difference between revisions of "Refined table"
| Line 21: | Line 21: | ||
==Sanity checks with the refined tables== | ==Sanity checks with the refined tables== | ||
| − | + | ||
| + | During a project, it is useful to check how an alignment is going. The ''refined table'' gives a couple of handy options to check it visually. | ||
| + | |||
===Checking the aligned particles=== | ===Checking the aligned particles=== | ||
| + | You can apply the computed alignment parameters into a few particles to check if they make sense. This is specially useful with membrane proteins. | ||
| + | |||
<tt>ddbrowse -p myProject </tt> | <tt>ddbrowse -p myProject </tt> | ||
will open {{t|ddbrowse}} onto the data and the last available refined table of project {{t|myPoject}} | will open {{t|ddbrowse}} onto the data and the last available refined table of project {{t|myPoject}} | ||
| Line 30: | Line 34: | ||
===Checking the orientations=== | ===Checking the orientations=== | ||
| + | You can sketch the positions and orientations of particles after an alignment iteration. This is useful when scanning how a set particles selected by [[Seed oversampling]] is evolving during the iterarion. | ||
| + | |||
Use {{t|dtplot}} with the {{t|oriented_positions}} option as {{t|profile}} | Use {{t|dtplot}} with the {{t|oriented_positions}} option as {{t|profile}} | ||
{{docfunction|dynamo_tableplot|dtplot}} | {{docfunction|dynamo_tableplot|dtplot}} | ||
Latest revision as of 10:15, 22 April 2016
The refined table is the result of the alignment iteration. Dynamo produces one refined table per iteration and reference.
It follows the Dynamo convention for tables. In particular, Dynamo should fill some columns in a refined table during alignment:
- columns 3 (marks if the particle was actually used for the average produced at the iteration)
- columns 4-9 (the alignment parameters)
- column 10 10 (the cross correlation coefficient computed for the alignment particle)
- column 34: In multireference projects, the reference number that the particle has been assigned to.
Contents
Accessing the refined table
The ddb command provides easy access to the results of the project. Here some examples of syntax
Display the name of the last computed table (by default, from reference 1) ddb myProjet:t -d
Display the name of the tables computed for all iterations at one given reference: ddb myProjet:t:ite=*:ref=2 -d
Read the refined table of iteration 3 into workspace variable myTable ddb myProjet:t:ite=1 -d
Sanity checks with the refined tables
During a project, it is useful to check how an alignment is going. The refined table gives a couple of handy options to check it visually.
Checking the aligned particles
You can apply the computed alignment parameters into a few particles to check if they make sense. This is specially useful with membrane proteins.
ddbrowse -p myProject will open ddbrowse onto the data and the last available refined table of project myPoject
Checking the orientations
You can sketch the positions and orientations of particles after an alignment iteration. This is useful when scanning how a set particles selected by Seed oversampling is evolving during the iterarion.
Use dtplot with the oriented_positions option as profile dtplot
