Hi All,
Thanks for all of the great suggestions--it was actually Ethan Merritt's
suggestions and pointing to the right Gnuplot documentation that really
worked for me. Gnuplot is actually pretty powerful, and can make quite nice
images. Again, thanks a million for the help.
Jacob Keller
---
Once upon a time I worked in a group that was interested in developing
crystallization in microfluidics. This was before the time that Fluidigm
existed and we had not heard of crystallization with the aid of microfluidics
at the time. We had good reason to try to make a system that was as smal
Once upon a time I worked in a group that was interested in developing
crystallization in microfluidics. This was before the time that Fluidigm
existed and we had not heard of crystallization with the aid of microfluidics
at the time. We had good reason to try to make a system that was as smal
do any of fffear/pirate/buccaneer use SIGFP in a significant/meaningful
way?
-bryan
On Wednesday 16 January 2008 13:27, Jacob Keller wrote:
> Hello all,
>
> It might just take you a few minutes to tell me how to do this:
>
> I have a set of data in three columns xyz (resid1, resid2, value), which I
> would like to plot as a "heat" or "color map" on the 2d rectangle formed by
>
On Wed, 16 Jan 2008, Jacob Keller wrote:
I would like to plot as a "heat" or "color map" on the 2d rectangle
[...] cannot figure out how to do this in gnuplot or anywhere,
consider gnuplot pm3d (not readily obvious for googling, is it)
http://t16web.lanl.gov/Kawano/gnuplot/plotpm3d-e.html
-br
Are you familiar with pm3d? I couldn't give the solution from the top of
my head, but
http://t16web.lanl.gov/Kawano/gnuplot/plotpm3d-e.html
seems a good source of information.
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 16 Ja
Hello all,
It might just take you a few minutes to tell me how to do this:
I have a set of data in three columns xyz (resid1, resid2, value), which I
would like to plot as a "heat" or "color map" on the 2d rectangle formed by
the values xy, and colored by z. Essentially what I want is a ~1500
sajid akthar wrote:
Hi All
Sorry for non CCP4 question. I want to make Pottasium Nitrate solution
of pH 6.9 (ofcourse for crystallisation trails only). I'm adjusting pH
by using NaOH. But it seems the pH is not stable after sometime. Is
there any good way to do it.
Thank you
Sa
Hi All
Sorry for non CCP4 question. I want to make Pottasium Nitrate solution of pH
6.9 (ofcourse for crystallisation trails only). I'm adjusting pH by using NaOH.
But it seems the pH is not stable after sometime. Is there any good way to do
it.
Thank you
Sajid
Now you can chat withou
First you cannot normally expect two in the same AU have the same
structure, so an over-weighted averaging may cause bias.
It is likely that a rigid-body refinement down to two molecules or
even domains may help improve in your case.
On Jan 16, 2008, at 8:47 AM, Sun Tang wrote:
Hello Ever
ni hao,
I have a question about how to improve the electron density. I have two
indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the
structure with PHASER and refined with CCP4i (Rfree = 0.29).
For the first molecule, the density is very good, but for the second one,
STRUCTURAL BIOLOGY OF WOUND HEALING
A 2 year postdoctoral position, funded by the French National Research
Agency, is available at the Institut de Biologie et Chimie des Protéines in
Lyon (www.ibcp.fr) to study the molecular mechanisms of wound healing and to
develop novel anti-scarring strategies
Hello Everyone,
I have a question about how to improve the electron density. I have two
indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the
structure with PHASER and refined with CCP4i (Rfree = 0.29).
For the first molecule, the density is very good, but for
You optimize that variable as well in scale-up.
That is the problem with nano-drop screening- sometimes it is near
impossible to scale up the drops. You have to re-screen around the
conditions (response surface methods can conserve experiments) because
the kinetics change so much between nano and b
Vaheh,
If I'm optimising in 24 well trays after a hit in 96 I generally use
sitting drop trays (cryschem) as a first step and try different ratios
of protein:mother liquor first rather than changing the protein
concentration. I know that sometimes the crystals stick to the plastic
but I use th
I have been using Phoenix for more than two years and so far there were
no issues with maintenance. Wash the needles and nano-dispenser before
and after the runs and you are good to go.
Electrostatic effects have been seen in a way of drops being positioned
on the side of the flat bottom plate, but
Regarding stochastic processes: to increase the chances of nucleation
one would like to have protein in the right nucleation zone for a
certain period of time.
If the drop becomes too small, the ratio evaporation surface/drop
volume changes. So, the nucleation zone might be reached within the
More recently, I've looked at all of the crystallization robot
vendors.
For single lab users, all of the systems work well. Systems like
the Hydra
or Mosquito are less automatic, but provide the basic functions for
crystallization trial setup. For more of a user facility with a large
number of
Oryxnano 50+50 nL
Demetres
Which, indirectly, brings up an interesting (but not relevant to the
Oryx) question.
Nucleation is a process that does have a stochastic aspect.
Thus, one could argue that compromising to 200-300 nl might be better
than either extremes of 50nl (too small volum
In our original work on a prototype, we used the Cartesian technology. We
were able to dispense 10nL+10nL drops with a large range of viscosities
without difficulty. The main issue was to wash the tips after use to
prevent clogging. That was with a system that could dispense 1nL droplets.
The prese
Hi all,
On Wed, 16 Jan 2008, Ian Tickle wrote:
I'm rather surprised that is the complete explanation, for the simple
reason that Perl (or any program for that matter) already inherits all
the environment variables from the shell in which it is run, including
PATH, CINCL, CLIBD_MON etc which wou
Hello Yadong,
This is what I would do in your position.
1) Integrate everything in MOSFLM
2) Enforce consistent indexing using POINTLESS (unless I am mistaken, there
are alternative origin(s) in p321)
http://www.ccp4.ac.uk/dist/html/alternate_origins.html
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/prereleas
PROTEROS is a leading service-provider for the preparation and
three-dimensional structural analysis of proteins for structure-guided
drug discovery. Our work contributes to fast and rational development of
new therapeutic compounds. Since its foundation in 1998, PROTEROS is a
continuously growing,
Hi there,
I have 3 incomplete data sets, collected from 3 single crystals, each accounts
for ~40% completeness. They have same resolution range, and randomly overlap
with each other a small portion.
Mosflm and Scala work well for all 3 separately. The 2 from same beamline have
very close stati
Oryxnano 50+50 nL
Demetres
David Briggs wrote:
I'll defend the honour of the phoenix... (again)
Bernhard Rupp 100+100 nl
Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl
Others..
Only time we have ANY problems is when the nano dispensing tip gets
clogged. Often a good wa
I'll defend the honour of the phoenix... (again)
Bernhard Rupp 100+100 nl
Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl
Others..
Only time we have ANY problems is when the nano dispensing tip gets clogged.
Often a good wash whilst still on the machine will clear the blockage.
D
Dear Bernard,
I do not have long experience using Phoenix. I tried the machine during a
couple of demonstrations I had chance to participate and also learned about
other people experience who used the robot (various MPIs and universities in
Germany and a couple of users from industry in Europe)
I'm rather surprised that is the complete explanation, for the simple
reason that Perl (or any program for that matter) already inherits all
the environment variables from the shell in which it is run, including
PATH, CINCL, CLIBD_MON etc which would be needed to run pdbset, refmac
etc. In fact so
Dear Rajan,
In addition to the estimates already mentioned, if you have access to Chem3D
(Cambridgesoft), you can calculate the Connolly volume (excluding solvent)
for any (preferably small) molecule, either drawn by hand or by input from
its coordinates. In ChemBio3D ultra, this is found in
It isnt a bad approximation for any organic compound to take the number
of atoms including hydrogens, and multiply it by 10A^^3
Eleanor Dodson
Rajan Pillai wrote:
Hi All,
Can anyone tell me any program that calculates voume of a ligand? Moreover,
is there also any program that can calculate th
Hi everybody,
I wonder why in lsqkab, the glycine residues have a rms value for their
side chains which are non null
(the same calculation done with CNS give about the same results for the
rms calculation, but with
null value for the rms of glycine side chains).
thanks a lot
nathalie
--
Dr.
Hi
A simple trick that small molecule crystallographers have been using
for decades is based on the average volume of non-hydrogen atoms
being about 18 Å^3 (this is close to being more-or-less correct for
C, N and O, and the presence of one or two S or P atoms usually makes
little differe
33 matches
Mail list logo
