User Tools

Site Tools


gpu_isac

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
gpu_isac [2021/05/08 00:34]
shaikh [Download & Installation]
gpu_isac [2021/05/08 00:41] (current)
shaikh
Line 113: Line 113:
  
   * Use the ''<nowiki>--</nowiki>CTF''  flag to **apply phase flipping**  to your particles.   * Use the ''<nowiki>--</nowiki>CTF''  flag to **apply phase flipping**  to your particles.
 +  * Use the ''<nowiki>--</nowiki>VPP''  flag with phase plate data. This flag may also be useful for non-phase-plate data, such as membrane proteins in membranes, or generally cases where low-resolution data may dominate the alignment. The ''<nowiki>--</nowiki>VPP'' option divides by the 1D rotational power spectrum of each image, or in other words "whitens" the Fourier data.
   * Use ''<nowiki>--</nowiki>img_per_grp''  to limit the **maximum size of individual classes**. Empirically, a class size of 100-200 (30-50 for negative stain) particles has been proven successful when dealing with around 100,000 particles. (This may differ for your data set and you can use GPU ISAC to find out; see below.)   * Use ''<nowiki>--</nowiki>img_per_grp''  to limit the **maximum size of individual classes**. Empirically, a class size of 100-200 (30-50 for negative stain) particles has been proven successful when dealing with around 100,000 particles. (This may differ for your data set and you can use GPU ISAC to find out; see below.)
   * Use ''<nowiki>--</nowiki>minimum_grp_size''  to limit the **minimum size of individual classes**. In general, this value should be around 50-60% of your maximum class size.   * Use ''<nowiki>--</nowiki>minimum_grp_size''  to limit the **minimum size of individual classes**. In general, this value should be around 50-60% of your maximum class size.
gpu_isac.txt ยท Last modified: 2021/05/08 00:41 by shaikh