Ji,
probably the oil doesn't work and the glycerol gets you into problems
with phase separation in 2.5 M AmS
I recommend sucrose or other sugars with AmS - 20-22% (w/vol) should
do and you get no phase separation
At the same time you may need to increase the AmS considerably - often
the
You could use salts such as LiSO4 for cryo-protection (also amm sulphate
with small crystals has worked to a degree with us, when nothing else
worked, also 1.6-1.7 M amm. sulphate was exchangable to 40% PEG 400 (very
quick), although with not so great results...).
which oil did you try? that
I will be out of the office starting 24.06.2008 and will not return until
25.06.2008.
I maybe able to reply to your message from the 03/06 till the 11/06. There
will be no replies from the 12/06 till the 23rd/06. Apologies for any
inconvenience.
PS: Dear ccp4bber's, it seems that my
Hi Ji,
Our lab has had good luck using sodium malonate to cryoprotect salt-
grown crystals. See:
Acta Cryst. (2003). D59, 2356-2358
Malonate: a versatile cryoprotectant and stabilizing solution for salt-
grown macromolecular crystals
T. Holyoak, T. D. Fenn, M. A. Wilson, A. G. Moulin, D.
Dear All,
After my enquiry a few days ago and some helpful responses, we are now
aware of two programs to calculate solution properties from atomic
structures (pdb files).
HYDROPRO (available for linux and windows):
http://leonardo.fcu.um.es/macromol/programs/hydropro/hydropro.htm
ref: J.
Dear all,
I apologize for the off-topic question.
I'm looking for some software that is able to read in (small
molecule) structure files (e.g. .pdb, .cif,..)
and subsequently outputs a listing of bond lengths AND 'environment'
distances for each atom within a certain radius.
Additionally,
Hi
SHELX should be able to do this if you convert your co-ordinates into
the appropriate format...
On 24 Jun 2008, at 12:30, Eleanor Dodson wrote:
It sounds like something the CCDC software might do?
Eleanor
DISTANG will do it for pdb input
Kristof Van Hecke wrote:
Dear all,
I
There is a program called XP in the Bruker SHELXTL system that
(amongst many other things) does precisely that (use the ENVI
instruction) taking symmetry equivalents into account. I suggest
that you find the nearest small-molecule crytallographer, maybe
she/he has XP (which has no relation to
Dear All,
Sorry for off-topic question. Does anyone have any experience in purifying
protein using pH gradient in Mono Q column?
I have been googling for a whole day, only one paper was found to mention
performing pH gradient in Mono Q, but in a mixture of amine buffering
species, which is a bit
This is on OSX Tiger 10.4.11 on a G5 machine.
Phaser 2.1.1, CCP4 6.0.2
Is anyone else seeing the following ?
In a feature that seems new-ish in Phaser, intermediate solutions get
culled after translation function and before packing tests:
(begin snippet)
Purge solutions according to highest
Hey Matt,
it seems to me that what you're asking for is chromatofocusing. See the
official GE documentation:
http://www6.gelifesciences.com/aptrix/upp00919.nsf/Content/WD:Chromatofocusin(260949098-R350)
The proprietary buffers are a bit expensive, but as you found out,
they're a bit
Thanks Guenter and Andreas,
Yea, I have taken a look for the Mono P before, I thought the material they
used in Mono P is basically the same as in Mono Q and I found the
bookProtein Purification Protocols: Second Edition by
Paul Cutler mentioned that phosphate buffer can also generate a
On behalf of the organizers, Maria Armenia Carrondo and Thomas R. Schneider
COURSE ANNOUNCEMENT - BIOCRYS 2008
Fundamentals of Modern Methods in Biocrystallography - 'What you
always wanted to know about crystallography but never dared to ask'
http://biocrys.itqb.unl.pt
4th - 11th October
Matthew,
You're not going to ruin your column, but you won't get great
performance either. Elution by pH change is a very common method,
but getting a really linear pH gradient is very hard. The Mono Q
matrix is a strong anion exchanger, meaning that it is insensitive to
pH changes,
Matt, there should be also a material called PBE94 for pH range 9 to 4
(and another one called Pharmalyte for high pH) to pack your own column.
It worked pretty well for our protein and is not in the high price
region of the MonoP column.
Best,
Guenter
Matthew Chu wrote:
Thanks Guenter and
Michael,
Well, why do you need to titrate the exchanger rather then the proteins
themselves?
MonoQ is a lot simpler to adjust pHwise, as with DEAE you actually
titrate both the matrix and the proteins.
Recommended buffers to use are Goods' (pKa from 8 to 6.15 at 20 °C) +
acetic acid (pKa
To the CCP4 community,
I have been trying to run PHASER to phase a nucleic acid structure by MR
using a partial template model. The problem is that symmetry-related molecules
generated from the output .pdb file coordinates spatially overlap with
extensive clashes. I understand from the
*The first Ghana Biomedical Convention* will take place in Accra- Ghana from
13th - 15 August 2008. Please if you are interested visit:
http://www.ghanabiomedicalconvention.org/
Note that everyone is invited to attend.
Sam
SANBI/NBN
South Africa
Thanks to those of you that replied.
The packing bug turns out to have been observed in Phaser 1.3 with
ensembles. We upgraded to Phaser 2.1 and the packing problem has
disappeared.
Thanks Randy.
Shane Atwell
Director, Crystallization
SGX Pharmaceuticals
10505 Roselle Street
San Diego, CA
Dear all,
I have used chainsaw for several times and no problem happened before yesterday.
When I used it last evening, the chainsaw couldn't run as usual. I checked the
log file and saw the error message as follow CHAINSAW: Chainsaw is having
trouble reconciling input pdb with sequence . In
Hi everyone,
can anyone tell me the protocol to revive human corneal cell lineor any
cell line which requires serum free media
i usually used serum based media initially.later switched it to serum
free media for subculturingonly in case of human corneal cell line
with the help of
Highly recommended:
Animal Cell Culture: A Practical Approach
by R. Ian Freshney (Editor)
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Exec
Sent: Tuesday, June 24, 2008 10:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] cell line
Hi
Hi folks:
Sorry for the off-topic nature of the following question, but I
thought this question (or more specifically, answers to it) might be
of general interest, given the current economic situation.
Has anyone had any experience using a headhunter to find either
consulting positions
Lets see. Bill Scott Publications in the last 5 years include (but
definitely not limited to):
Nature: I
Plos Bio: II
Chemistry Biology: I
Nature: II
Science: I
Cell: I
JMB: II
And you are considering getting out of academia? What about this makes
me worry?
James
On Jun 24, 2008, at
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