Hey Scott,
I personally can only recommend motic. You get a stereo miscroscope with
video camera/usb/svideo for way under $2k. We bought them with a lot of (mainly
useless) aceessories for $1800/ea from VWR. They are not as sturdy/comfy as
leicas (my favourite if money doesn't matter) but exce
Some proteins can be purified at room temperature. Others would be degraded
or may lose 'competency' (however you wish to define the latter). As a rule
of thumb, *most* proteins will not be hurt by exposure to +4C, but e.g.
detrimental protease activity should follow the normal kinetic rules and
sl
Hello all
I've made a mask by MAMA from a PDB file. I also used command "Atom_fit" to
check that all of the atoms were covered by the mask.
But after converting the mask to ccp4 format and opening in COOT, the mask was
too small, only covered half of the model. The mask was cut along two axis.
Hello people,
Thank you very much for so many replies you've gone to for me including
direct emails. This is a little summary of all the replies as a token of my
appreciation.
> It would take too long to list all the options here -
> however I would look at the earliest stages of your expressi
Dear Scott,
If you're looking for rock-bottom prices I would try scouting a few used
equipment dealers. Also consider asking major brand sales people to quote
you for a 'floor model' or a 'demo model' - very often these are deeply
discounted.
With respect to brands - I personally have tried
Lots of things change with wavelength and absorption is one of the more
prominent ones, but in the end its all just path lengths and Beer's law,
so the exact answer depends on the geometry. For example, if you are
talking about a flat detector 200 mm from the crystal, then 2 A spots
with 1 A
Starting a new lab and looking for an inexpensive stereo microscope to
support my crystallography. Any thoughts or recommendations? Would like
for it to have a way to take a photo of the crystals either through an
eyepiece or dedicated camera port. As any new lab, a cheap option won't be
bad.
Sc
The internet is incredible...within about 2 minutes, a few people had read
my post and found that Aldrich was a broken link...there is only one "l"
in Aldrich.
www.sigmaaldrich.com
or
www.sigmaaldrich.com/sigma-aldrich/home.html
Please forgive me for the error and the multiple post.
Kris
-
I have been asked about a supplier. I know of at least 4:
1. Aldrichwww.sigmaalldrich.com
Fomblin Y LVAC 14/6Cat # 317934-100G100g
2. Lancaster/Alfa Aesar
www.alfa.com/CGI-BIN/LANSAWEB?WEBEVENT+L0178567F6B740600C68505B+ALF+ENG
Hello All,
I did diffraction with the exact same sample at 1 Å and at 1.54 Å and
noticed that the higher-resolution data from the 1 Å source is more
intense relative to the 1.54 Å source after normalizing cumulative
intensity between the two data sets. Is this effect from air
absorption o
Hi Fengxiale,
Have you tried no cryoprotection? 10% PEG4K is probably too low but you may
get lucky. Since your crystal is already in PEG, you may try increasing the
concentration of the PEG or try just plain ethylene glycol, which may be more
gentle on your crystal than sticking it in glyce
You can always give this one a try:
http://www.xtals.org/crystal_cryo.pdf
Artem
"Nothing is built on stone; all is built on sand, but we must build as if
the sand were stone"
Jorge Luis Borges
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Fengxi
There is a ellipsoidal truncation and scaling server you might want to try.
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
~L~
__
Lari Lehtiö
Pharmacy, Department of Biochemistry and Pharmacy
Åbo Akademi University,
BioCity, FIN-20520 Turku
F
Hi,
We have been trying to obtain fructose 2,6 bisphosphate (F-2,6-BP) for
quite sometime now. Sigma has been trying to synthesize F-2,6-BP for over a
year now and has still not managed to produce large enough quantities. I would
be very grateful if someone could recommend any other possibl
Hi
Thanks for your quick response.
a) I have used CNS script cns_to_o.inp and then used the CCP4 COORDCONV
utility with
convert file in PDB to PDB option and input the unit cell information.
(have tried Xplor to PDB option earlier, it failed with input error).
b) Then I run refmac
...and I prefer to use PFPE (perfluoropolyether, trade name FOMBLIN) as an
oil since it is less viscous, has no reactivity and is a low temp
lubricant that freezes easily. Small molecule crystallographers have used
it for years.
Kris
-
Kris F. Tesh, Ph D
Directo
Have you tried to grow the crystals in the presence of small amounts of
cryoprotectants?
For example, use sucrose, glycerol, ethylene glycol, trehalose, glucose,
sorbitol, various salts in the crystal growth.
One can use concentrations of the additives in the 1% to 4% (w/v or v/v)
range. The
Hi Justin,
may be I mis-understood your question, but can't anisotropic scale
factor that is the part of the total structure factor (as defined in
phenix.refine for example and most likely in the other programs):
Fmodel = scale_overall * exp(-h*U_overall*ht) * (Fcalc_atoms + k_sol *
exp(-B_s
One thing that I have had work in the past is just increase the
percentage of PEG. I think something around 30-35% may work for
PEG4K, maybe a little higher. Most PEGS will work as a cryo
protectant if the concentration is high enough.
Also as mentioned before you could try stepping up
The CNS script cns_to_o.inp will convert CNS .mtf
files to .pdb files. You can edit the CNS form using the CNS web
interface and then run the script from the command line. Alternatively,
I think the CCP4 program COORDCONV will convert XPLOR/CNS files to PDB
format (I haven't done this, however.
Dear All;
I am working with a data set which is anisotropic. The resolution
limits are ~ 2.75 by 3.45 A. The I have integrated (using Mosflm) the
data out to 2.75 A, the data therefore includes a mix of real (I/sig
>>1) and imaginary (I/sig ~1) data past the 3.45 A resolution bin.
I am c
Hi all,
How to convert CNS coordinate file to PDB file format that can be used for
refinement in
refmac. Is there any utility in CCP4 or other GUI based interface that can
convert CNS output
file to PDB .
Thanks .
Manoj
Penn Sate University
Biochemistry
State College
PA
Dear bulletin-boarders...
Does anyone know of a good (UK?) source, where I can buy some carba-NAD?
I would like to use it in some co-crystallisation experiments.
I've looked in the 'usual' places - i.e. Sigma-Aldrich, but can't seem to find
it anywhere.
Many thanks in advance,
Antony
We have had very good success with fragile,
crack-prone crystals by doing gradual soaks in increasing glucose.
Besides the osmotic pressure/solvent composition changes induced by
cryopreservation, another reason crystals crack is drop dehydration.
You can minimize dehydration of exposed drops b
It is Arp waters which doesnt support these space groups I believe..
REFMAC5 seems to accept everything..
And Arp-waters is pretty out of date - cot probably does a better job
in positioned fully occupied waters.
Eleanor
David J. Schuller wrote:
For the latter, P21221, you could reindex t
Hi all,
A non CCP4 question, the cryo diffraction without protein crystal had
absolutely no ice ring. But when I transferred protein crystal from the
sitting drop to the cryo, there was ice ring in diffraction pattern.
My doubt is whether water shelled around the crystal led to this ice ring,
and
Dear Fengxiale,
I would suggest two thing you can try:
1) shock-freeze the crystal: pick it up from the crystallisation plate
with the mounting loop and only briefly (<=1s) dip it into the
cryo-condition, then freeze it in a bath of liquid nitrogen.
I would try both glycerol and PEG400.
- try
Dear All,
Could you please help me solve this problem?
I have a sensitive crystal, the mother liquor is 10% PEG4k+ 100 mM
Tris-buffer pH 8.5, crystal is big and good but very sensitive, when i put
it in cryoprotectants, cracking happened. First i used artificial mother
liquor + 25% v/v glycerol,
Hi all,
Is there a server to quickly check, given an antibody structure, if
the CDRs are in the canonical structural classes (except for the H3).
I've already looked here (http://www.bioinf.org.uk/abs/index.html).
I'm also looking for a latest reference on the canonical structures
although I have
Hi
Google is a wonderful thing. I'm afraid I did it the old-fashioned way
and looked at a paper copy of the original publication (in the
author's office), and that didn't have page numbers...
On 1 Sep 2009, at 02:28, 张强敏 wrote:
Using "Leslie, A.G.W., (1992), Joint CCP4 + ESF-EAMCB Newslett
Another consideration is that you may want to run some (most)
experiments in the cold and others at higher temperatures.
We had a case of a cold-sensitive protein that could only be
effectively purified at 20 degrees Celsius - and the cabinet where we
have our FPLC in with variable temperatu
Postdoctoral Position in Structural enzymology of bacterial pathogens
A postdoctoral position is available for a highly motivated individual
at the Department of Medical Biochemistry & Biophysics, Karolinska
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