Hello,
I am experiencing a weird problem with B factor refinement (individual,
isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A
resolution. The ADP values after the refinement are very very low, less
than 2 and sometimes 0. I am getting the same result with and without
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Dear Demetres,
does this affect all atoms, or only a few selected ones?
Did you compare with refmac5 (for e.g. input script errors), or did
you reset the B-factors to a reasonable value (e.g. 20-30) prior to
refinement? pdbset can do this
Dear Tim,
this affects all atoms and yes I did reset the B-factors to 20.00 prior
to refinement. I have not tried REFMAC but now I will give it a try
since phenix does not seem to do the job.
best
Demetres
On 2/11/2012 1:34 μμ, Tim Gruene wrote:
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That sounds like the bug in Phenix.refine v1.8 that a few of us encountered -
updating to the latest release will help.
Actually wasn't so much a bug but a feature, albeit not the best one
imaginable. Anyone using older v1.8 versions should update.
---
Phil Jeffrey
Princeton
On Nov 2, 2012,
Joao,
I am using the latest version of phenix 1.8.1-1168
1.8.1-1168 should not have that problem.
If you suspect there is still a problem, you can send me the data and model
files off list, explain what exactly the problem is, and I will have a look
right away.
FYI: there is Phenix mailing
In my opinion Rpim is not related directly to anomalous signal, so perhaps that
is why there is some confusion.
Also I think some folks confused Rpim with Rrim. The latter is also called
Rmeas. But once again, these are not related directly to anomalous signal. I
do not find Rpim very
