For detailed examination of this topic, see:
Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner,
T. (2000).
Active-site gorge and buried water molecules in crystal structures of
acetylcholinesterase from Torpedo californica. Journal of Molecular Biology
296, 713-735.
Well - years ago I wrote a program called watertidy to do just this -
but it asigned waters as OH0 OH1 OH2 with a according to what atom it
was H bonded too, and those names are not now permitted..
My way now is to read in a completed homologous structure - use SSM to
fit it over the new one -
At deposition the PDB runs a script that renumbers authors' waters according
to a scheme based on the residue they are nearest from N to C terminus along
each chain. This renumbering started when waters were assigned to
macromolecular chains rather than getting a chain id of their own. I
Dear all,
this water discussion is flowing increasingly towards a place where I
feel a bit out of my depth.
What is the convention for numbering water molecules? Is there
preference for:
- putting waters into a separate chain (W for water or S for solvent)?
- splitting waters according to
While there is no systematic study (I think) on this we have observed RH
control systems and concentration of solutes can have the same effect -
Photosystem 1 crystals were dehydrated by transferring them from 20% to
40% PEG6000 resulting in a smaller unit cell and better diffraction
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Dear Andreas,
I am not sure there is a convention, but there has been a decision.
When you deposit a structure with the PDB, they place all ligands
including water molecules to the respective nearest macromolecular
chain. I found this rather annoying
Dear Elise,
Try the 3Dss server (http://cluster.physics.iisc.ernet.in/3dss/). You can
superimpose up to 20 structures and look for invariant waters.
Cheers,
Uli
---
dr ulrich gohlke
staff scientist - macromolecular
We've had that leak as well some time ago. Dismantle and reassemble it is the
trick. Just a slight angle when tightening it will lead to that problem. This
is usually the case because of overtughtening the reservoir to the main part of
the machine. Keep it always straight when closing it again.
This is to be answered by PDB people, who definitely read BB :)
Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts
this out
Eugene
On 30 Oct 2013, at 12:09, Andreas Förster wrote:
Dear all,
this water discussion is flowing increasingly towards a place where I
Dear all,
Apologies for such a retro and non-biological question, but would
anyone have a photograph of an Arndt-Wonacott rotation camera that he/she
would be willing to share? I collected data on the first two prototypes in
the early seventies, then on one of the first commercial models,
Dear all,
We seek to appoint a Post-doctoral Training Fellow to join the newly
established Armenise-Harvard Laboratory of structural biology at the
University of Pavia. The group will focus on the molecular characterization
of extracellular ligand and receptors involved in synapse formation using
Dear Gerard -
Here is one picture, but I'm afraid it's quite small and not good quality:
http://books.google.com/books?id=S9PPHvJ8otMCpg=PA28
I assume the camera is that object with the multiple circles in the left
center of panel A?
Also, these folks seem to have one in their collection:
Is the prototype shown Figure 1 from
U. W. Arndt, J. N. Champness, R. P. Phizackerley and A. J. Wonacott
A single-crystal oscillation camera for large unit cells
J. Appl. Cryst. (1973). 6, 457-463
http://dx.doi.org/10.1107/S0021889873009210
There is, of course, a photo in The Rotation Method in crystallography, by
Arndt and Wonacott, which currently fetches over $245 on Amazon...
On 30 Oct 2013, at 16:05, Gerard Bricogne wrote:
Dear all,
Apologies for such a retro and non-biological question, but would
anyone have a
Bob Sweet has a powerpoint presentation but it took a long time to download the
file
A good source for used books is used.addall.com which
searches many used book dealers. A copy of this book is
listed there for about $60 US and is shipped from the UK.
Frances
=
Bernstein + Sons
*
Hi
Or you could look at using something like an Apple TV connected to a wall
mounted flat screen monitor to stream via wifi (which may be better suited to
fast data rates than bluetooth). Roku or Chromecast might be cheaper
alternatives to the Apple TV, but I know almost nothing about them.
Dear Daniel,
Thank you very much! That is the kind of picture I was hoping for.
Thanks to you too, Bob, for your Powerpoint presentation that contains other
interesting pictures of the major instruments that made MX possible.
Finally, many thanks to the authors of all the other
Elise - after looking into a related problem for some time, I've come
to the conclusion it's a bit harder than it seems. Two obstacles:
(1) there is no good coordinate system for partitioning the overall
solvent volume (fraction of unit cell not occupied by protein density)
into suitable
Gerard,
I have the original rotation method book in my office, and it might have the
picture that you are looking for. I will check in the morning.
-Mark
___
Mark A. Saper, Ph.D.
Department of Biological Chemistry, University of Michigan Medical
Thanks for the help, the issue is solved. Here a short summary in case anybody
else has the same problem:
1) Add pointer atom in Coot NH2 and create link to C-terminal residue
2) create cif file with correct link description
3) modify LINK record in PDB to correct residues/ link name
4) refine
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