Bug #17
open
Xmipp symmetry names are not correctly implemented in pipeline
Added by Neil Voss over 14 years ago.
Updated almost 13 years ago.
Affected Version:
Appion/Leginon 2.0.1
Description
for example, octahedral is 'O' in Xmipp and by default we use the EMAN name 'oct', we need to add an additional column in ApSymmetryData to have Xmipp names. This would then have to be fixed in Denis' create a new database code and for all project databases'
- Target version set to Appion/Leginon 2.1.0
- Affected Version set to Appion/Leginon 2.0.1
- Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
- Show in known bugs set to No
- Assignee set to Anchi Cheng
Anchi, do you think this is necessary? didn't we just decide that we will standardize the gui on EMAN naming for now, and in the future move to industry standards? do we need a column in the db for each method's standard?
I put this in as a method to communicate with Xmipp. You select icos the EMAN style symmetry on the web, you need some way to tell Xmipp 'I' to get icos symmetry in Xmipp. I was thinking we could look up the translation in the database. Should be easy to implement.
Eman name is not unique even in apSymmetryData.
Since Amber is using the "name" field (the one including axis description) for the refactoring when it comes to symmetry choice, the package specific name conversion is done per package in apRefineJob subclass for now. The bigger problem is that I am not sure of matching of the names in different packages when it comes to O and I since some of them are not in point group standard axis anyway. Thus far, I am only doing ones I can be sure in apRefineJob subclasses.
For example, I don't know what I1 and I2 orientations are in Frealign.
Xmipp is especially bad(?) for they include more symmetry than proteins can have....
Yes, we should still do the matching in a more permanent place, but we can't do that in the database, yet, unless we settle for a partial list. In a way, it will always so since point group has infinite members....
- Target version changed from Appion/Leginon 2.2.0 to Appion/Leginon Future Version
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