Hi Mohamed,

Did you check the model after autoSHARP? If yes, then how does it look like? ‎I 
guess your solution given by autoSHARP was not correct one and it couldn't 
build the proper model. That is the reason why you see a lot of dummy atoms. I 
would say the dummy atoms are not useful at all. Because if they are, bucaneer 
could have been able to build the proper model. So, it's better to try again 
another phasing determination rather than spend time with a dummy model.

Thanh N

  Original Message  
From: Mohamed Noor
Sent: jueves, 13 de octubre de 2016 16:35
Reply To: Mohamed Noor
Subject: [ccp4bb] autoSHARP: Am I on the right track?

Dear all

Following on the previous thread on Fe-SAD, there is a solution(?) from 
autoSHARP with an OK-ish map and model. A quick refinement with phenix.refine 
gave me an R/Rfree of 28/31 % (2 A, although for the phasing run I told 
autoSHARP to use only up to 2.5 A). However, the model was filled in with about 
6000 dummy atoms (DUM) plus some regions with just Gly. I did provide a 
sequence file, so not sure why it didn't build them in. When I deleted all the 
DUM atoms, the R/Rfree increased to about 48 %.

I am wondering, are the positions of DUM atoms correct and I just need to build 
it manually somehow?


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