Woops, sorry. There was a typo in my response. here it is again
without the typo.
B factors are 78.96x the value of the mean square variation in an atom's
position. The square is the important part of how you scale them. Lets
say you have static disorder in the crystal lattice, and that
What do you mean by “unique”? In the absence of anomalous signal, I+ and I-
should be the same, so are not independent, and it doesn’t make sense to count
them separately. Even if there is some anomalous signal, it is generally small
on average compared to the whole intensity, so I+ and I- are
Hi Asmita,
Try running your different crystal structures through PDB_REDO. That should
normalize the B-factors to some meaningful values for comparison.
Best wishes,
Avinash
Hi Ed,
your suggestion makes perfect sense to me, and it's trivial to add an
option to do what you want. This will be available in next Phenix nightly
build (clearly not tomorrow given today's power outage).
Command line: use "write_map_coefficients_only=True" (by default is is
False).
B factors are 78.96x the value of the mean square variation in an atom's
position. The square is the important part of how you scale them. Lets
say you have static disorder in the crystal lattice, and that gives
every atom an rms variation of 0.5 A relative to their ideal lattice
positions,
On Wednesday, 02 August, 2017 21:58:07 Asmita Gupta wrote:
> Hi,
>
> Thanks for the response!
>
> What I have are crystal structures of the same protein in multiple
> conformations, solved by different groups. I wanted to calculate the
> residue-wise B-factors for each of these structures and
Dear software users,
All LBNL crystallographic servers will be off line due to a power shutdown,
taken as a precaution due to a nearby wild land fire in the Berkeley
hills. This will affect PHENIX, LABELIT, CCTBX and other servers. We
apologize for the downtime.
Nick
Nicholas K. Sauter, Ph.
Hi,
also keep in mind that the total model structure factor used in refinement
and anywhere where model-to-data agreement needs to be evaluated (such as
maps or R factors) is:
Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else)
where ktotal ~ scale * exp(-h*Uoverall*h_transpose)
Just to clarify, how do you use the extra columns in this scenario? My
suggestion was to have the output file that includes only the map
coefficient columns, so you still can look at the map. IIRC, FP/SIGFP
columns from refmac output are actually modified from the input (scaled
with Boverall),
Hi,
Thanks for the response!
What I have are crystal structures of the same protein in multiple
conformations, solved by different groups. I wanted to calculate the
residue-wise B-factors for each of these structures and compare how the values
are changing for corresponding residues in these
Hi,
This might look as a very fundamental question. I have a dataset of crystal
structures better than 3.5Ang resolution. For a qualitative analysis, I
want to compare the residue-wise B-factors in these structures, but due to
different procedures adopted in refinement and scaling, I understand
On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote:
> Just to clarify, how do you use the extra columns in this scenario? My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map. IIRC, FP/SIGFP
> columns from refmac
On Wednesday, 02 August, 2017 12:09:35 Asmita wrote:
> Hi,
>
> This might look as a very fundamental question. I have a dataset of crystal
> structures better than 3.5Ang resolution. For a qualitative analysis, I
> want to compare the residue-wise B-factors in these structures, but due to
>
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