Dear all,
we also have a lot of "fun" with LINK records when taking deposited
PDB structures into BUSTER refinement. Sometimes (but not often) there
are missing LINK records, but the vast number of problems is due to
erroneous LINK records added by annotation software it seems (based on
a cut-off
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I also should backtrack a little. I assumed that Anandhi has good
data reduction with good statistics, no data problems (such as twinning),
a good molecular replacement solution, and refinement stuck, but he
didn't give any of those details. What are the R and Rfree values, the RMS
bonds & angles
Okay, I'm an idiot. The letter did say molecular replacement. I
have no excuse for being so blind.
I do stand by my statement: I don't see that an average B factor of
82 A^2, by itself, indicates any serious problem with a model at 2.65 A
resolution.
I have generally found that the ave
Did I miss a follow-up letter with more information? All I've seen
is that Dr. Anandan said that there was a model based on 2.65 A
resolution data with an average B factor of 82 A^2. Does this fact
alone call for weeks of work attempting to remove model bias? Dr.
Anandan didn't even say this
Hi Tristan,
Erroneous LINK records happen quite a lot and used to be the combination of
aggressive annotation software and depositors not paying attention to the
comments from the annotators. They make up a large fraction of the bug reports
I have sent to the PDB over the years. They are usuall
Hard to comment on PHEIX refne but check these things: such results must
either mean your molecular replacement solution is wrong or there is
something wrong with the data.
Refinement packages will always try to match the Mean B factor to the
Wilson plot B so I think the problem must be before refi
