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.
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?
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?