Dear Lu Zuokun,
since you can use the output mtz-file from ArpWarp for model building,
but not for refinement, there is no need to include the Rfree flag in
its output file. Maybe the omission is a deliberate caveat to the users
to pay attention to this.
Best regards,
Tim
On 10/20/2014 04:41
Dear Colin and Tim,
But ARPwARP uses REFMAC5 for refinement, does this means that REFMAC5 uses
all reflections as working set?
How to validate that the refinement is not over fit?
Best wishes!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
At 2014-10-20 17:38:58, Tim Gruene
When you chose the option “Do not use the Free R flag”, then you were telling
Refmac not to use cross-validation and therefore to use all reflections as the
working set.
My experience (doubtless very limited compared to the ARP/wARP developers) is
that it’s significantly better to use the
Dear Lu Zuokun,
The option you mention do not use the Free R flag, tells ARP/wARP to do
refinement without using the R-free flags, so it does not seem strange to
me that it would output a file without those labels.
I don't know why this would be a good idea, though, if you want to continue
Dear Lu,
The MTZ file produced at the end of the ARP/wARP protein model
building is created by Refmac and contains the following:
1. New columns created for the built model: (FC, PHIC, FC_ALL,
PHIC_ALL, FWT, PHWT, DELFWT, PHDELWT, FOM,
Dear all,
I was using ARP/wARP in ccp4i, the input mtz file certainly has free R
flag, but the output mzt file doesn't have the free R flag label?
I chose do not use the Free R flag in the ARP/wARP GUI. Can anyone tell me
what's wrong with this?
best reagrds!
Lu Zuokun
--
卢作焜
