From: CCP4 bulletin board On Behalf Of Matt McLeod
Sent: Saturday, October 1, 2022 2:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PAIREF - Warning - not enough free reflections in
resolution bin
Hey everyone,
Thanks for all the suggestions there are a few different things I can try now.
T
If AIMLESS is throwing out a lot of reflections, something is wrong. You should
look closely at what is being rejected, in the list of “ROGUES” and the plot of
position of outliers on the detector face
DIALS (probably dials.scale) has its own rejection scheme, as does XDS
There are two basic re
Hey everyone,
Thanks for all the suggestions there are a few different things I can try now.
The data is very aniosotropic (STARANISO might help) in regards to how the
crystal diffracts and I think changing the bin size will help specifically with
PAIREF (its an warning so it completes the run
Hi Matt,
you cite the message "WARNING: There are only 40 < 50 free reflections ..." but
in the next sentence you write "This error ...".
Being a program developer myself, I'd like to point out that there is a
difference between a warning and an error. An error typically makes the program
stop
Dear Matt,
Your data past 2.5A is awfully weak, and wont contribute much to any map
you calculate. Each term at the outer resolution will have a very low
weight.
I sometimes cling to the belief that the weak data may help the B factor
refinement, but there isnt much evidence of that. There is a fee
Is the data anisotropic? This would explain the strange processing
statistics beyond 3.0 Angstrom. If using Dials directly it is worth
looking for abnormalities with the reciprocal lattice viewer.
I've seen similar issues with the completeness being low, when data is
weak in one direction, despit
Dear Matt,
thank you for asking. I am bit confused how you set up the PAIREF run.
In paired refinement, data are added step by step - going to higher
resolution, i.e. lower d_hkl. So the merged data in the PAIREF input
should not be cut to much. The data statistics look from DIALS quite
stran
Hi all,
I am having a bit of trouble with PAIREF. I am trying to determine the
resolution cutoff of a dataset which has a high Rwork (0.223)/free (0.275)value
for the resolution (2.24A). I have truncated this data further to 2.4A and the
R values get better but the electron density maps do no
