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Yi, Nogales says that the Head density is most probably occupied by the Rrp44 NTD. The head density is 20Ang apart from the Body. How does it reconcile with the crystal structure by E. Conti, where Rrp44 looks like a compact particle?

rbmaxtrans = 2.00
fbmaxtrans = 2.00
rbmaxrot=0.04

Riccardo, I could not remember exactly what you explained to me about these parameters. Would you mind writing it up here if possible? Nice to take a note.

Thanks!

The comparative model for Ski7 is a bit puzzling! The paper says it is "a comparative model of Ski7 259–747 structured domain generated using Phyre2". But the name of the file (Ski7_3izq_modeller_vmd.pdb) suggests that Modeller and VMD were used. Which is it? @Pellarin can you clarify? The file doesn't contain any headers typical of either Phyre2 or Modeller.

Was 3izq used as a template for this modeling as the name suggests? If so, can you point me to the alignment used? We should make sure this model is reproducible.

The RMSFs for all other clusters look OK, but for cluster.0 of the Rrp6 modeling, all the RMSF values are reported as zero (e.g. Rrp6.analysis/kmeans_weight_500_2/cluster.0/rmsf.Ski6.dat). That can't be right, can it?