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gpu_isac [2021/02/22 11:01]
fschoenfeld
gpu_isac [2021/05/08 00:41] (current)
shaikh
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 All done! All done!
 +
 +<note>During installation GPU ISAC links itself to the SPHIRE GUI and can be called from there like any other SPHIRE program!</note>
 +
  
 ===== Running GPU ISAC ===== ===== Running GPU ISAC =====
  
-An example call to use GPU ISAC looks as follows:+When calling GPU ISAC from the terminal, an example call looks as follows:
  
 <code> <code>
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   * 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.
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 ---- ----
 +
 +**GPU ISAC v2.3.4**
 +
 +  * Updated the installer to automatically link GPU ISAC to the SPHIRE GUI.
 +
 +**GPU ISAC v2.3.3**
 +
 +  * Internal changes only.
  
 **GPU ISAC v2.3.1 & v2.3.2 (hotfix releases)** **GPU ISAC v2.3.1 & v2.3.2 (hotfix releases)**
gpu_isac.txt ยท Last modified: 2021/05/08 00:41 by shaikh