Changes between Version 59 and Version 60 of NTTData

Timestamp:

Oct 21, 2021, 1:45:13 PM (4 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -370 +370 @@
 - What colors to use for 7+ chains? Phil: can we have a palette repeat?  Eric, yes among the other possibilities. Phil likes the interpolated one but wants to check with Darrell and get back to us. Tom G suggests doing something fancier based on symmetries, maybe as a longer-term goal. Phil: another fancy coloring is by domain.
 - What to do when map level produces disconnected surface bits, with only a very small bit left after hide dust? Elaine: Doesn't that mean the level is wrong?  Tom: may be correct level for step 1 but gets fragmented at the higher step automatically used for larger data. Even a single piece may be too fragile if it's a thin shell. Phil: printing software automatically thickens a too-thin shell. More discussion of just using step 1 (too many vertices is problematic for printing), map smoothing, iterating threshold adjustment vs. "measure volume" with "includeMasked false" (may be too slow).  May need to leave this one to manual interactive adjustment. Chimera/X initial default is to put 1% of voxels inside contour. Tom G has fancier ideas like struts, or binning (e.g. bin 4 instead of step 4, more like smoothing, but requires also lowering threshold to avoid more fragmentation). Phil: measure volume of largest bit at step 1 vs 4, then possibly bin. Maybe enhance bin to use max instead of avg, then do that instead of adjusting step.  TomG: needs evaluation; binning with max vs. avg may give more grid artifacts.
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+== 10/21/2021 ==
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+Phil, Philip, Darrell, Meghan, Neta Filip-Granit (project manager for cryo-EM at NIAID); Elaine, Eric, TomG, Zach, Greg
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+Darrell: we may ask you about cryoEM issues in the future, since we know you're closely working with UCSF cryoEM folks. Neta: Recent advances include motion correction (Agard lab's MotionCor2), current challenge is data screening. TomG: EM is used in many different ways, including tomography.
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+UCSF team introduces itself.
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+Meghan: shouldn't we talk about progress on the 3D pipeline?  Some emails went back and forth.  
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+Philip: for EMDB it tries to get metadata (recommended threshold). Seems to be using FTP, is that for each entry?  TomG: it chooses different locations. For Philip it is choosing the European site, ends up using FTP. TomG: will make a ticket to see if there is a newer https method available. 
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+Philip: Some GLB files are causing errors.  TomG: send example(s) please. We are not including texture coordinates, so it doesn't make sense that there is an error message complaining about them.
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+Elaine: other progress, Eric modified script to deal with structures missing many atoms, and correctly handle NMR ensembles. He also added a non-fattened ribbon output.
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+