Dear Frank,
it's not a secret that phenix.refine ALWAYS writes total B-factor into
ATOM records, there are strong reasons for this and this is clearly
stated in the manual.
Reasons to write total B-factor:
1) Easy analysis (Easy color by B-factor in graphics: no prior model
manipulations are
Dear Pavel and Frank
It is my recollection that one of the primary goals in the
creation of the PDB format was the interchange of information
between software packages. While it has certainly failed to
meet that (difficult) goal it has been useful at least in the
interchange between refinemen
Hi Pavel
All your reasons are there for the convenience of the
*crystallographer*, mine are for the end user (=unsuspecting biologist)
-- who doesn't know TLS even exists (none of used to), never mind about
Hirshfeld's test and how it relates to TLS (I didn't), and certainly not
how run it (I
> 2) All you need to reproduce the R-factors are the ATOM records and
> structure factor formula (and not ATOM records, PDB header with TLS
> records that sometimes may be lost or manipulated and specific
> converting programs to add TLS contribution). Also note, that not all
> programs extract
On 3/29/2008 12:57 PM, Winn, MD (Martyn) wrote:
2) All you need to reproduce the R-factors are the ATOM records and
structure factor formula (and not ATOM records, PDB header with TLS
records that sometimes may be lost or manipulated and specific
converting programs to add TLS contribution).
Hi Frank,
Hi Frank,
All your reasons are there for the convenience of the
*crystallographer*, mine are for the end user (=unsuspecting biologist)
-- who doesn't know TLS even exists (none of used to), never mind about
Hirshfeld's test and how it relates to TLS (I didn't), and certainly not
ho
This is exactly what phenix.refine does: it puts all together so you are
not expected to have any knowledge about magic TLS matrices in PDB file
header, about right programs to convert one into another and so on. In
contrast, if one split things apart:
Yes, but no non-crystallographer cares a
On 3/29/2008 1:37 PM, Frank von Delft wrote:
This is exactly what phenix.refine does: it puts all together so you are
not expected to have any knowledge about magic TLS matrices in PDB file
header, about right programs to convert one into another and so on. In
contrast, if one split things ap
I think that it is essential that the PDB file that actually gets
deposited contains ANISOU records that have had the isotropic
contributions added already, and that the B on the atom record is
one third of the trace of the orthogonalised Bij tensor that can be
derived from the ANISOU record, j
I suspect there's not going to be consensus on anything except that
there needs to be a standardization regarding deposited TLS
parameters.Probably the first step is to convince the pdb to not
throw away the record describing what's actually in the B-factor column.
In my (probably unimp
Hi,
On Sat, Mar 29, 2008 at 07:57:44PM -, Martyn Winn wrote:
> Anyway, these are all different representations of the same thing,
> and should work equally well so long as you know which you are
> using. The scariest thing from the last thread was that our attempt
> to document it with a REMAR
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