Good old Val-Lys. I've noticed in the recent overhaul of the
PDB they adopted the convention that any peptide less than three
amino acids in length is now HETATOMs instead of ATOMs. This may
be screwing up Coot's ability to link the dipeptide. I suggest
you edit the PDB file to change these k
Clemens Vonrhein wrote:
Hi Jim,
On Fri, Jan 22, 2010 at 09:11:00AM -0600, Jim Pflugrath wrote:
I do not know the effect myself, but the idea of "vibration fee" has been
tossed around a while.
What? I'll have to pay for vibration now as well? Are you collecting
that personally? Or is i
Graduate Course - Neutron Scattering techniques in Structural Biology
Oak Ridge TN, June 7 – June 11, 2010
Dear Colleague,
The completion of the Neutron Spallation Source (SNS) and the cold source at
the High Flux Isotope Reactor (HFIR) at the Oak Ridge National Laboratory
(ORNL) opens a new er
If Eddie were a bit more self-promoting, he might have pointed out this
paper:
http://journals.iucr.org/d/issues/1997/06/00/gr0718/gr0718.pdf
Snell et al. (1997). Acta Cryst. D 53, 747-755.
Where they found that crystals growing in space could "tell" when the
astronauts were exercising (low fre
Hi Jim,
On Fri, Jan 22, 2010 at 09:11:00AM -0600, Jim Pflugrath wrote:
> I do not know the effect myself, but the idea of "vibration fee" has been
> tossed around a while.
What? I'll have to pay for vibration now as well? Are you collecting
that personally? Or is it just another scheme to save so
We are going to be a pretty unpopular bunch if this thread concludes that we
need to set off fire alarms in order to nucleate our crystals.
:)
Sean
Hi ,
Maybe the lower frequency of the earthquake vibrations or the
handling helped your crystals nucleate. I would assume that even the
resonance frequency of the linbro plates are low, and may cause
disturbances in them. However, fire alarm systems usually are of a much
higher frequency (shril
I guess the crystals will be "safe but freaked out".
I think handling the crystal trays is a process which would much more
influence the crystal growth.
Do you ask because you have frequent fire drills or your colleagues have a
affinity for arson?
Sorry for the jokes, could not resist.
Cheers,
When working on tobacco Rubisco in Los Angeles, we got the best crystals
of the activated form of the protein after small earthquakes (4-5 on the
richter scale). However, as people in the lab. noticed, this earthquake
parameter is somewhat difficult to control. Handling the linbro plates
sometimes
I would be more worried about why the alarm is going off. In theory
the alarm should only go off when tested or when you have a real fire,
in which case I wouldn't worry about how it effects my crystals. Most
places only test the alarms once or twice a year.
There are "silent" alarms avai
On nucleation I'm not sure if there is any effect - I suspect you've got
far more trouble from Brownian motion. For growth low frequency
vibration (picking up the tray and putting it down) has much more
influence than high-frequency (e.g. fans or motors). The liquid acts to
damp most of the high-fr
I do not know the effect myself, but the idea of "vibration fee" has been
tossed around a while. I believe that no vibration reduces the amount of
nucleation that one might get, thus a vibration-free environment is
detrimental when screening for hits. If you already have a method to grow
crystals
If your crystals exploded, the alarm would provide warning to other
residents of the building.
--
===
All Things Serve the Beam
===
Dear all,
Does anyone know the effect of a fire alarm placed in the same room where
one grows crystals?
(1) On trays placed inside styrofoam boxes
(2) On trays placed inside an incubator which has not been tested as
vibration free.
Thank you.
Jackie Vitali
Megha,
If you want to prepare your sample at a pH below the pI, you will want
to use a cation column.
Enzymes at pH's below their pI have an overall positive charge. Cation
exchange is a column which has a negative charge, thus it will bind to
positively charged proteins.
I would suggest looking at
Dear John Campbell (not you, the real John Campbell whom I know and who
would never do such a thing as to send SPAM, the "other" John Campbell),
Thank you very much for your kind offer. May I suggest that you fly to
Haiti immediately and offer these commodities there at once, for free?
They ar
Dear All,
The email about the network sales company which appears as if sent from me on
22 Jan is a scam and was certainly not sent by me. I hope that there will be no
more of these but I guess you will need to be aware that they might appear
again in some form.
Best wishes,
John Campbell
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton
> Sent: 21 January 2010 08:39
> To: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Refining against images instead of only
> reflections
>
> It is interesting and rel
Dear all,
we would like to ask coot to fit the Val-Lys dipeptide of a thermolysin
structure.
We read in a PDB-file with the VK-fragment and run the "Other Modelling
Tools->Find Ligands" tool.
Unfortunately coot rips the pair apart and only places the valine into the
density, the lysine is simply
The Protein Data Bank in Europe (PDBe http://www.ebi.ac.uk/pdbe/) is
looking for two Scientific Database Curators to work as part of the PDBe
Annotation Team on the annotation of preliminary data submissions to the
PDB/EMBD. Details of the job and application are given below. Please get
in touc
Hi all,
yesterday i have tried annealing, no significant improvement.
Thank you so much for all those suggestions.
Summary:
1. check diffraction on RT.
2. dehydrate crystal, many methods
3. try annealing
4. grow crystal in presence of cryo
5. try smaller crystal, sometimes small crystal is bette
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