AlignProjections: Align projections of PDB/MRC volumes with class averages
This program will align a PDB file or a 3D MRC with a 2D class average stack (.mrcs). Aligning projections with class averages serve as a validation of your 3D reconstruction. OR, this will tell you if your PDB model agrees with your class averages.
Why should you use this?
When you want to align a PDB or MRC volume with a stack of class averages (or projections in a stack).
E.g., let’s say you have these class averages (.mrcs format) and you’d like to know if it matches a 3D reconstruction:
(These are beta-galactosidase class averages from RELION tutorial)
How does this program run?
This program will use SPIDER for the following steps:
- Forward project input 3D map
- Align each class average with the best matching projection
- Display class averages alongside best matching projection (rotated in the registry)
Aligning PDB file:
If you’re aligning a PDB file, the program will convert the atomic model into density using e2pdb2mrc.py (from EMAN2) first, then align projections with class averages.
How to run this program on COSMIC²
- Input for job > Upload a PDB file OR a 3D volume using web browser upload
- Important: If you upload a 3D volume, the volume must have the same pixel size and dimensions as the class averages.
- Selected when creating a task > Upload a stack of class averages from any software (RELION, cryoSPARC, etc) that are in .mrcs format using web browser upload
- You can download the class averages from cryoSPARC by clicking the download button for class averages > Download outputs > ‘Blob’
- Resolution limit for PDB upload – this resolution is used to filter the converted PDB to MRC volume
- (Advanced) Angular sampling – this specifies how finely the projections will be sampled from the 3D volume
- (Advanced) Pixel size of class averages – input pixel size here, otherwise the program reads the pixel size from the header
- (Advanced) B-factor to apply to converted PDB file – a positive value here will also act like a low pass filter to help the atomic model agree with your averages in appearance
The program will output the class averages shown alongside projections as .mrcs or .png file:
The output stack will output images in pairs:
class average #1 + matching projection #1 ;
class average #2 + matching projection #2 ;