Dear colleagues,
We have encountered a problem with our dynamic light scattering instrument
DynaPro from Protein Solutions (New Jersey) and would like to solicit your
suggestions and advices. The instrument was purchased about six years ago.
In the past years, the intensity (Cnt/s) has decre
Just spent an hour trawling docs, BBs (recent threads) and logs to
figure out what the hell my B column is telling me (phenix vs refmac vs
pdb).
Oh dear, it's a disaster area, quite Heissenbergian... the most
important number (uncertainty) is itself unknowable:
* Phenix writes total ADP, Ref
Dear Yingjie,
This does not answer your question directly but we had a similar problem
with our DynaPro purchased from Protein Solutions. Most likely this is
due to an optics misalignment or a dead laser. Protein Solutions'
products are now available in the US through Wyatt Technology
(www.wya
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
Just to point out that the CCP4 wrapper to SSM "superpose" allows you to
specify residue ranges to consider - very useful for multi-domain proteins.
See the -s switches in
http://www.ccp4.ac.uk/dist/html/superpose.html
I'm not clear if this was your issue.
Cheers
Martyn
-Original Message--
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
ANISOU records imply that individual anisotropic B-factors were refined.
This will cause problems when you try to redo the final refinement: you add
loads of parameters all of a sudden. Using ANISOU records may give you more
reliable information about the B-factors, but not about the refinement.
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
On 3/29/2008 1:25 PM, Robbie Joosten wrote:
ANISOU records imply that individual anisotropic B-factors were refined
This is not always true.
Pavel.
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
Yep, agree completely!
My point was that if you try to bypass the TLS parameters, then you still need
to retain the
anisotropic component somehow. But I wasn't advocating it.
I believe the simplest and most honest thing to deposit are the parameters of
your model,
viz the TLS parameters and the
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, here's what triggered my earlier rant:
I took a pdb from phenix.refine back into refmac, with same TLS
definitions, but leaving the ANISOU cards in (accident). I ran this
through TLSANL, asking for total B.
Refmac has left the ANISOU cards, but all zero except the first
element. ATOM B
Some comments:
- We (the PHENIX developers) are working with the PDB to come up with
a more
streamlined deposition of TLS information for PHENIX. There are
some other
issues that need to be resolved first that have slowed this down a
little.
- I am in agreement with George (not unusual
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