I'd support BR's position. Why the compelling urge to fill every blob with
atoms? Density should only be modeled when its interpretable. One can comment
about the blob in a paper, and perhaps even show maps for the region,
indicating that there might be something there if its believed to be a
f
I think there is at least one more option here (relevant at least in some
rare cases):
Identifying what that something is likely to be can be significant and may
advance your career
Of course it is important to present supporting or otherwise evidence for
the interpretation. As already discussed,
On Feb 3, 2010, at 4:15 PM, Ethan Merritt wrote:
So far as I know, the PDB/RCSB folks do not even look at these
columns.
So it comes down to a question of individual non-PDB programs.
Which program were you wondering about?
I guess the big ones, CCP4, CNS, coot, O, pymol, phenix, solve/resolv
On Wednesday 03 February 2010 15:59:26 James Stroud wrote:
> Hello All,
>
> In typically comical fashion, the PDB specification 3.2 at
> http://www.wwpdb.org/documentation/format32/sect9.html
> leaves out columns 67-76 for ATOM and HETATM records.
>
> Since I can only conclude that SEGIDs mus
Hello All,
In typically comical fashion, the PDB specification 3.2 at http://www.wwpdb.org/documentation/format32/sect9.html
leaves out columns 67-76 for ATOM and HETATM records.
Since I can only conclude that SEGIDs must be one of those "grey
areas", I thought I'd make a multiple choice su
Mark J. van Raaij wrote:
> as it appears to bear near the guanidine group of an arginine, I would
> suggest it is a partially occupied and disordered sulphate and/or
> phosphate.
> whether this is practically modellable is another matter, a sulphate at
> occ. 0.5 is an option, or putting a water wi
On Wednesday 03 February 2010 10:04:36 Pavel Afonine wrote:
I always suggest to run these refinement jobs and see which
> one gives the best result:
>
> 1) TLS + individual isotropic ADP refinement (tls+individual_adp);
> 2) TLS + group individual ADP refinement (tls+group_adp);
I do not think
Yeah, only the RealD goggles, the ones that look like these and that
are given out at "standard" (not IMAX) movie theaters:
http://www.google.com/products?q=reald+3d+goggles&scoring=p
will work. Several users brought back the IMAX goggles that look like
these (might be yellow):
http://www.3dglas
Dear Ed,
Tightly restrained refinement will be equivalent to
torsion angle parametrization, since bonds and angles are essentially
fixed (but dihedrals are not).
Simply not true. Think why -:) Hint: in restrained refinement the weight
applies to all terms - bonds, angles, torsions, etc... S
I agree with many others: this is quite possibly sulfate or phosphate.
If collected at 1.54A the anomalous map should help identify the
presence of sulfur. Sulfate or phosphate may be present at lower than
full occupancy. I would refine everything else you reasonably know in
the model (includin
General remark if I may
Putting nothing in:
no significant effect on model and life in general
Putting something potentially wrong and misleading in:
could be detrimental to your career
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Katja
Schleider
Sent: W
On Wed, 2010-02-03 at 18:26 +0100, Mark J. van Raaij wrote:
> as it appears to bear near the guanidine group of an arginine, I would
> suggest it is a partially occupied and disordered sulphate and/or
> phosphate.
If it's a sulphate, a look at the anomalous map should show something.
--
Thanks very much for the reference; I have always wondered about precisely
this relationship (how much salt = how much PEG). Interestingly, the authors
note that down to PEG 1500, the MW of the PEG does not change the
corresponding salt values very much. I wonder whether anybody did this for
MP
Hi Katja,
What I personally do in such a situation is to start to fill the density
by water oxygen atoms, refine a bit (the position plus the isotropic
temperature factors) and then compute a new map. Usually it has cleared
up somewhat, thus allowing you to find out what it really is. This is
as it appears to bear near the guanidine group of an arginine, I would
suggest it is a partially occupied and disordered sulphate and/or
phosphate.
whether this is practically modellable is another matter, a sulphate
at occ. 0.5 is an option, or putting a water with a remark in the pdb
that
Hello,
FYI the 3D glasses distributed for viewing the Avatar movie can be used to
view structures in COOT using the Zalman monitor.
Regards,
Jay
Maria Jamela R. Revilleza, Ph.D.
Research Fellow
Molecular Biology Section
Laboratory of Immunology
NIAID/NIH
Building 10, Room 11D10
10 Center Drive
Pavel,
> - In general you are free to decide what you name a domain: it can be
> a residue, its part or the whole structure.
> - What would be "main" and "side" for non-amino acid molecule, like a
> whatever ligand?
I don't see how my freedom to explicitly define the terms I use in a
post is rele
Hi folks
(1) I missed out one of the fixed bugs in the latest release - the
"WAIT" command in iMosflm now works properly, so you can start
processing while you are collecting and let iMosflm worry about
whether the images have been collected yet.
(2) This is a little embarrassing!
Mosflm
Dear Colleagues,
The 2nd Circular for the International Symposium on Diffraction Structural
Biology (ISDSB2010)
is now available to download from the Conference website:-
http://www.synchrotron-soleil.fr/images/File/ISDSB2010-2ndcircular-010210.pdf
Best wishes,
John
Professor J R Helliwell DSc
On
An RA position in membrane protein structural biology is available in the group
of Dr Bernadette Byrne, Imperial College London. The position is funded for two
years by GlaxoSmithKline as part of an industrial collaboration focusing on the
structure determination of clinically relevant G-protein
Zitat von Imre Toeroe :
Hi,
this might be relevant here:
http://scripts.iucr.org/cgi-bin/paper?S0907444995000436
Yes! thanks for the link.
Imre
Clemens Grimm wrote:
regardless of what such a (kinetic) calculator will calculate at the end -
we will have to feed it with data of the type "
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Pete
> Sent: 02 February 2010 01:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: how to supply the following twin operator to detwin?
>
> The determinant of the matrix is zero, so
> i
Hi,
this might be relevant here:
http://scripts.iucr.org/cgi-bin/paper?S0907444995000436
Imre
Clemens Grimm wrote:
regardless of what such a (kinetic) calculator will calculate at the
end -
we will have to feed it with data of the type "vapour pressure vs.
concentration and temperature" of s
regardless of what such a (kinetic) calculator will calculate at the end -
we will have to feed it with data of the type "vapour pressure vs.
concentration and temperature" of substance X. Even without a whole
simulation tool for the kinetics of a vapour diffusion experiment this
will alread
BCA/CCP4 XVII Summer School in Protein Crystallography
Biochemistry Department and St. Edmund Hall, University of Oxford.
5th-10th September 2010.
Scope.
The BCA Summer School is a combined taught and practical course intended
primarily for students and researchers new to crystallography. I
Hi,
Instead of calculating the drop composition, there is a simple device,
refractometer, which you can use to measure the actual composition of the
drop (based on the refraction indices of the components). Some of us even used
it in the old days. It's possible that with nano-size drops some
I would like to add that contrary to popular belief, MPD would have to be
treated as a volatile in the example you give below. It vaporizes, although
very slowly, as can be proven by leaving a 1uL drop of it in open air for a
couple of days.
Cheers,
Jose Antonio Cuesta Seijo.
"Jacob Keller" wro
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