Differences

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--- gpu_isac [2021/02/22 13:34]
fschoenfeld
+++ gpu_isac [2021/05/08 00:41]
shaikh
@@ Line 71: / Line 71: @@
 <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 =====
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   * 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>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.