gt;>> In generally I like the treatment of carbohydrates now as branched
>>> polymers. I didn't realise there was an exception. It makes sense for
>>> unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as
>>> these might change during
Hi all,
I was confused when I saw mysterious new glycan chains emerging during PDB
deposition and spent quite some time trying to find out what was wrong with my
coordinates. Then it occurred to me that a lot of recent structures also had
tens of N-glycan chains. Finally I realized that this
Hi all,
If anybody is interested in non-viral stable expression, we have a
piggybac-based, doxycycline-inducible system. It is the reference 40 in the
lentiviral paper that Tomas directed to. We’d be happy to distribute the
plasmids.
Zhijie
> On Jan 25, 2020, at 3:26 AM, Tomas Malinauskas
Hi Orly,
REMARK 290 should be the easiest way for generating symmetry mates. Other
routes are just going to give you the same results. As Jonathan already pointed
out, the symm ops do not garantee that the symm copies are close to each other.
The most simple-minded solution to this problem wou
There are CCD modules (often come with lenses, which can be taken off) sold on
Amazon, eBay or aliexpress (or even better, Taobao) costing USD 20-40. These
modules should be capable of taking full HD movies (MPEG or YUV2 compressed) at
30fps these days. Some may allow 120fps@640x480 or promise h
Hi Jonathan,
We discussed about VAX floats last November:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811&L=CCP4BB&O=D&P=63307
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811&L=CCP4BB&O=D&P=65015
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811&L=CCP4BB&O=D&P=65531
In short
Sometime ago when I was watching a Youtube video on magnetron I learnt that at
least at at certain point of time the antenna port of the magnetron was sealed
using beryllium oxide ceramic(probably for its high thermal conductivity). The
video maker warned that this ceramic was extremely dangerou
Hi Jan,
As Paul pointed out, you can use COOT to accomplish what you want. Particularly
you can take a look at the following functions in section 6 of the COOT manual
(these are in scheme):
(set-map-mask-atom-radius radius)
(mask-map-by-molecule imol-map imol-model invert-mask?)
(transfo
Hi Jan,
Sorry I didn't read your script earlier. If you change your mapmask command to
output a map instead of a mask it may work for you:
mapmask \
mapin 2mol_2mFo-DFc.map \
xyzin 2mol_B.pdb \
MAPOUT B.map \
<< eof
border 2
eof
then you should get a map that covers the whole molecule
Hi Jan,
I guess you might be seeing a flat cut surface on the maps? It might be that
the map’s extent is not covering the protein molecule, which is usually the
case. When you rotate crystallographic maps it is usually no longer possible to
take adjacent unit cells to continue the density on the
Hi Nicola,
0.1-1mM Cysteine, GSH or BME will work fine. You can also try using very fresh
TEV without reducing reagent (or store it with BME and remove the reducing
reagent by some column just before use). Depending on how concentrated the
stock is, diluting it 3-5x could also sufficiently red
Hi,
I believe that one can put a 50-100uL drop of fresh SigmaCote (in a tube cap)
with the glass pieces (surface well exposed), sealed in a dedicated (because
the container will be coated too) container (air-tight lunch boxes). After a
while the SigmaCote vapor should react with the glass and
PCA?
On Jan 3, 2019, at 3:41 PM, Reza Khayat
mailto:rkha...@ccny.cuny.edu>> wrote:
Hi,
Happy new year to all! A bit of an off topic question. Does anyone know of a
method/program to extract the most distinct "n" (n>2) sequences from a sequence
alignment? Thanks.
Best wishes,
Reza
Re
Yes, we have also seen some indication that overdriving the expression can
cause problems. In our cases this may range from bad aggregations or loss of
expression. Since we use induced stable cells we simply reduced the doxycyline
levels.
Zhijie
> On Dec 14, 2018, at 1:13 PM, "r...@mrc-lmb.cam.
Hi Tomas,
Some thoughts:
a) I guess the thermodynamic drive for all part of this small ectodomain to
fold into a single lowest energy conformation is not very strong. The cells
can’t know that the little artificial domain is supposed to be a monomer when
the oligomers are also sufficiently hydro
are quite feasible for MTZ files (not maps because we can
put anything into MRC/ccp4 map). Yes, the idea is to try all possibilities
until we can recover miller indices that look normal.
Zhijie
From: Nicholas Devenish
Sent: Wednesday, November 14, 2018
rpret it as half bytes!
Zhijie
From: Nicholas Devenish
Sent: Wednesday, November 14, 2018 8:54 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie,
Looks like we both had the same thoughts!
On Wed, Nov 14, 2018 at 1:
Hi Nick,
Our LE outputs are exactly the same. Rmerge=100.0%!
Zhijie
From: CCP4 bulletin board on behalf of Nicholas
Devenish
Sent: Wednesday, November 14, 2018 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Eleano
It's also said here, at the end of file :
https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf
"add 1 to the left, with the binary point"
0.1.
From: CCP4 bulletin board on behalf of Zhijie Li
Sent: Tuesday, November 13, 2018 7:4
4:54 PM
To: Zhijie Li
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie
It's definitely a factor 4. The code is in subroutine QTIEEE in the Fortran
source I mentioned previously at this line:
See line:
A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2
If you
Hi Ethan,
Thanks for the information. My guess is that in MTZ only F-float is expected,
because it is the only 32bit form?
Zhijie
> On Nov 13, 2018, at 3:44 PM, Ethan A Merritt wrote:
>
>> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
>> If somebody is g
with Convex, Cray, Fujitsu, or VAX reals/strings?
> I’d be interested to see what those files actually look(ed) like.
>
> // Best wishes; Johan
>
>> On Nov 9, 2018, at 18:38, Zhijie Li wrote:
>>
>> Hi all,
>>
>> On linux there are a few good GUI HE
Hi all,
On linux there are a few good GUI HEX editors. Here I’d like to recommend
BLESS, which conveniently displays all possible numerical interpretations of
the four bytes under cursor. It also allows the user to switch between big
endian or little endian through a checkbox. Unfortunately all
Hi,
At high concentration (1-2%) the published saturating SDS:protein binding ratio
is about 1.4:1 by weight, that is roughly one SDS molecule per two aa on
average. It is dense but not that dense to prevent any further interaction.
More importantly, as a quite hydrophilic small molecule SDS
Hi Kevin,
a)
If your goal is merely to display EM maps, then UCSF Chimera, COOT,
pymol, etc. should all do. The EM maps are saved in the MRC format (.mrc
or .mrcs). Despite a different extension and some minor differences in
the headers, the MRC format is essentially the same format as our
e
Smith:
One should expect to see ladders each separated by 1 nt in such cases.
Mohammed:
My suggestions:
1) running at 70V seems low. I do not see a reason for not using higher
voltages. 200Vx45min should be OK. IT is better to not let the BPB front run
out of the gel - so that you know whether
Hi Gustavo,
If I understand you correctly, you are concerned about N-glycans
(N-glycosylation) on your proteins. According to your description, you
have 2 protein molecules in each ASU, each bearing one potential
N-glycan site. Then there are only two N-glycan sites you need to build
for each
Hi Vandna,
Assuming you have two copies, chain A and B.
In UCSF chimera:
1) open two copies of the pdb (model #0 and #1)
2) in command line, type:
match #1:.B@CA #0:.A@CA showMatrix true
Besides moving model #1 chain B to model #0 chain A, the match command
also outputs the r
Update: to get transparent background in GIF:
Chimera command file (now saves PNG with transparent background by
adding "set bgTransparency"):
close all;open #0 ABCD.pdb;
set bgTransparency;
~disp;ribbon :.a;
movie record directory "D:\mov_temp\" format png pattern frame_*;
turn y 1 15;wait;
Hi Shanti,
To get more control, you can use Chimera to generate the frames, save
each of them as PNG, then process and re-assemble the frames in
photoshop to make GIFs. The command line toolbox Imagemagick is also a
great way for making GIFs (shown below).
Step1 generating the frames
Mod
Hi Bernhard,
I guess you knew all these and is really asking for people's experience,
but please excuse me to start from the theory: N-glycans in eukaryotes
are known to be involved in glycoprotein folding in the ER. They allow
the nascent protein to get into the calnexin/calreticulin cycle in
Hi Chen,
I followed instructions on this page and it seems to be working:
http://www.geo.mtu.edu/geoschem/docs/putty_install.html
One thing I think is worth mentioning is that in Putty-connection-SSH-X11, I
put localhost:0.0 instead of 10.0, as for putty itself, it is requesting from
Xming for
Hi Vijay,
I am not sure if I understand you correctly. If you want to align by the two
nucleotide in two GTPase structures, you can simply do it in COOT using the
“LSQ superpose” function. You need to fill in the chain id and residue number
only for the nucleotide and choose “all atoms”. Unless
Hi Ivan,
In simple words: superdex is a few generations newer than sephadex. Main
difference: superdex is a physically and chemically, tougher medium.
Among all GE healthcare beads (or the ones I know of), superdex offers the best
resolution and mechanical strength (thus higher flow rate, very
The methods part of the 2008 nature paper also mentioned the two earlier,
high-res structures 1F39 (1.9 A) and 1LMB (1.8 A), which together cover
almost the whole strucutre except the linker regions.
I wonder, in such situations, is it a good practise to use the high res
structures, either as
Smith,
As Ian said, mtzdump can give you some clues, but will not solve your problem.
The file that mtzdump could not read apparently has changed length due to some
sort of insertion. The other file that mtzdump could process has the correct
length and the stats look reasonable, so it might be
Hi Ian,
Unix/Linux uses a single byte 0A (the linefeed character) as the line end
marker for text, while DOS/Win use two bytes 0D 0A (carriage return + line
feed). Old Mac systems use 0D. (what a mess!)
So a simple UNIX to DOS operation should expand every 0A in a file to 0D 0A:
perl -pe 's/\n
cursor should
land on the M of “VERS MTZ”.
You can find descriptions of the MTZ format here:
http://www.ccp4.ac.uk/html/mtzformat.html
Zhijie
From: Smith Lee
Sent: Thursday, March 05, 2015 3:46 AM
To: Zhijie Li
Subject: Re: [ccp4bb] how to recover my data
Zhijie,
Is any mtz editor? I
nchain and 2 for CAs
add_lsq_match(25,35,"B",25,35,"D",2)
apply_lsq_matches(0,1)#assuming imol 1 is
the moving one and imol 0 is the reference
Zhijie
-Original Message-
From: yanfeng zhou
Sent: Thursday, February 12, 2015 9:03 AM
To: Zhijie L
Hi Oarabile,
Coot allows you to align structures by selected atoms:
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/docs/coot-faq.html#How-do-I-do-a-superposition-on-just-a-part-of-my-structure_003f
I guess what you are trying to do can be accomplished by the “multi-range LSQ
superposition”
: Zhijie Li
Sent: Wednesday, January 21, 2015 2:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water
Hi Jacob,
I would agree with Nat. I think with the 3A data and the local environment,
putting a Cl there is only justified by the need of supressing a peak in the
difference map
Hi Jacob,
I would agree with Nat. I think with the 3A data and the local environment,
putting a Cl there is only justified by the need of supressing a peak in the
difference map. Yes the peak can really be a Cl or a water or a mixture of the
two (I would like to do an experiment with my Cl conta
Hi Chen,
Here is what I think:
Assuming a crystal is perfect and is being shot at 0 K, then the maximum
resolution one experiment can achieve is limited by the wavelength of the
X-ray. It can’t be better than the half-wavelength under the normal
experimental setting (minimum d=lambda/2/sin(90)
Hi Rohit,
If it is of some significance you may consider replacing NaCl with KI or NaI in
your crystallization condition and collect a dataset at 1.5-2 Angstrom. The
Iodide anomalous signal might be of some help for identifying Chloride binding
sites.
Without further evidence for a Cl ion, unl
: Sampson, Jared
Sent: Wednesday, January 14, 2015 3:48 PM
To: Zhijie Li
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Adding a residue with an insertion code
Thanks to Paul and Zhijie for the suggestions.
In the past, I’ve also renumbered everything from 1 (using pdbset) for the
duration of
f the residues are consecutively numbered (Calculate > Renumber residues),
and are assigned the same chain ID (Calculate > Change Chain ID), Coot might
surprise you and link them on its own.
On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li wrote:
Have you done it?
1) Click “add residu
Have you done it?
1) Click “add residue...”
2) Click that “real space refine zone” button.
You will see what will happen.
From: Dialing Pretty
Sent: Wednesday, January 14, 2015 9:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal
Dear
Hi Xiao,
I would poke the crystal with a piece of glass fiber or an oocyte needle to
make sure it is not salt. Some protein crystals can be a little tough
(rubber-like), but they react to poking very differently from rocks (salts) and
will eventually shatter. So far I have found this test to be
Hello,
My apologies for sending the previous post to the wrong BB.
Zhijie
-Original Message-
From: Zhijie Li
Sent: Friday, August 08, 2014 11:10 AM
To: R.D. Oeffner ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [phenixbb] local BLAST server
Hi Rob,
The BLAST nr database (fasta format) can
Hi Rob,
The BLAST nr database (fasta format) can be downloaded from the NCBI ftp:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
As I remember it is the nr.gz file. When unzipped the file is called "nr".
According to BLAST the nr database does contain PDB entries.
http://blast.ncbi.nlm.nih.gov/Blast
Hi Mintu,
I suggest using purified whole protein for ESI-MS. You will get a series of
protein peaks (if the substitution is not 100%, which is often the case), each
differ for 47 Dalton. You can determine how many Se each peak corresponds to if
you know the molecular weight of your protein. The
Hi Bernhard,
I too suspect that it is some kind of metal chelating reagent causing the
problem (possibly used in medium for carrying Fe2+, as the free Fe2+ is toxic
to cells). One simple test would be to load a liter of the unused medium to the
Ni2+ column and see what happens. Do you concentra
I beg to differ on this:
"Also, passive screens have a pol-filter in place, the fine lines of which you
will observe on a white background, the more disturbing the closer the viewing
distance to the screen is. So, for general office applications (writing text),
the screens are less useful. "
Our
Hi,
Two things i would like to add:
1) Due to the dependence of A280 on amino acid composition, a simple
two-wavelength 280 and 340 or 320 comparison is not very ideal for
determining the scatter component of the UV absorption of protein/protein
aggregate particles (the usefulness of this sim
Hi Debasish,
I would first use some of those crystals to make seeds and grow some new
crystals so that I would not lose the crystal. Dehydration, even done
systematically (eg,
http://www.mitegen.com/mic_catalog.php?c=jenCrystaloptdehydrate), may or may
not improve the diffraction. Like most ot
note: the same applies to UCSF Chimera, where the volume data
(maps) control also requires you to specify the cut off or gradient in real map
values instead of RMSD.
Zhijie
From: hongshi WANG
Sent: Wednesday, February 19, 2014 3:47 PM
To: Zhijie Li
Subject: Re: [ccp4bb] Can not see density
Hi Richard,
I am not sure if this is what you are looking for: second order nonlinear
optical imaging of chiral crystals (SONICC). It is not based on a
computational algorithm but the nonlinear optical property of chiral
crystals to double the wavelength when illuminated by intense light.
S
Hi Zhongzhou,
For laptops, the passive stereo (Zalman mode) would be the easiest way to go.
All you need to do is to plug that monitor to the VGA port of you laptop. The
halving of the vertical resolution under stereo mode only affects reading the
characters, which can be solved by setting the
Hi Dimetry,
The difference between LINK and LINKR can't be explained better:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html
Older versions of COOT used to not display the LINKR record, but now the
newer versions display both LINK and LINKR records as dotted bonds. I assume
that
It seem the LINK line I provided eariler was chopped by the email system.
Here it is again:
LINKRC1**MAN*C***1*OG**SER*B*912MAN-SER
Simply replace each * with a space and change the residue IDs.
Also to clarify the procedure of using refmac to generate the
Hi Dmitry,
COOT does have the MAN-SER linkage record in its monomer lib, but it won't
detect the bond for you. It also haven't provided an interface for the user
to specify the bond type yet.
The COOT procedure you described is perfectly fine for generating a generic
covalent bond record for a
Hi Engin,
Thanks for the information! I didn't realize that O-glycans can also be
specified as specific linkages like N-glycans. Those two extra angle
restraints should be helpful.
Zhijie
-Original Message-
From: Engin Özkan
Sent: Thursday, November 21, 2013 1:00 PM
To: Zhij
Hi Dmitry,
I think the best way is not to make a new monomer. MAN-SER and MAN-THR
linkages do exist in the ccp4 monomer lib. If you simply build a mannose
with its O1 removed and put the C1 ~1.4 Angstrom to the OG of the serine I
think refmac should be able to detect the linkage. When this hap
Hi Danilo and all,
A little trick for the glutaraldehyde "staining": you can hang a 1-2uL drop
of 25% glutaraldehyde (or the most concentrated stock solution you can find)
besides your crystal drop in the vapour diffusion chamber. The
glutaraldehyde will get into the crystal drop via vapour di
Izit is an aqueous solution of methylene blue, which you can prepare simply and
cheaply. Look here:
http://www.ysbl.york.ac.uk/ccp4bb/2000/msg00387.html
One word of warning: not every crystal stains. I found poking crystal with hair
or glass fibre to see if it cracks or breaks is more reliable
Hi Tom,
Yes, SC can be used for calculating protein-small molecule ligand SC. Simply
put the ligand and protein on two separate chains. You probably need to edit
the $CLIBD/sc_radii.lib file to add some atom radii for your ligand. For
example:
ABC N* 1.65
ABC C* 1.90
Zhijie
--
Hi Ed,
I guess by "24mL SD200" Peter meant the Superdex 200 10/300 column, which
most of us should be quite familiar with. According to GE healthcare, a new
Superdex 200 10/300 GL column should have TP >25000/m. For comparison, a new
Superdex200 16/600 PG, which uses bigger beads, has TP >1300
Hi Kavya,
If I understand you correctly (from title and text), you meant your negative
FoFc was around your ligand, is that right? I wonder if this is a case in
which the ligand has an occupancy below 1, but was modeled as 1, so the
refinement program had to give it a high B factor to compensa
Hi Jahan,
Maybe you are using a new model of BiaCore. Our old BiaCore X never cares to
tell us how to do our experiment. However if your RU did go below that of the
empty chip, then maybe you really didn't get anything conjugated.
The pH 3.8 condition is not good for the amine coupling reactio
r the gel and spend the 1-5 hrs there,
your initial conditions are lost anyways.
Zhijie
From: Careina Edgooms
Sent: Thursday, March 28, 2013 3:03 AM
To: Zhijie Li
Subject: Re: [ccp4bb] off topic, BN PAGE
Hi Zhijie
Thanks for the helpful reply. The attractive thing about BN PAGE (if it work
Hi Careina,
BN PAGE can be affected by many factors. Considering the complexity and the
chance of winning and the amount of information you gain even when you win, I
do not recommend fighting it.
BN PAGE, like other gel-based methods, requires that your complex is fairly
stable - not having a
Hi Alex,
The CCP4 package you downloaded seems to be a prebuilt binary package for the
X86_64 architecture. You do not need to compile yourself - and you can't
without the source code. Running ./configure is for configuring the compilation
environment before running "make" to compile source cod
PM
To: 'Zhijie Li'
Subject: RE: [ccp4bb] column tube
Dear Zhijie,
I am looking for the external clear plastic tube of
Bio-rad UNO Q1 Column 720-0001
Column information:
http://www.bio-rad.com/prd/en/GR/LSR/PDP/d825a6ab-49cf-4140-91c3-ea131c886b74/UNO-Monolith-Anion-E
Hi George,
What is the plastic tube? Is it part of the end adaptors or it is part of the
tubing? What type of plastic it is? If you can provide a photograph of the
broken part maybe someone can give you more useful suggestions.
Zhijie
From: George Kontopidis
Sent: Wednesday, March 20, 2013
Hello,
We have a curious situation here: after upgrading CentOS 6.3 to 6.4, COOT runs
slowly every time after the "go to atom" command is executed - every rotation
of the molecules takes nearly 1 second to finish. But if the "go to atom"
command is never sent then the speed is normal. A COOT ru
Hi Xianchi,
How did you treat the control flow cell? And what is the composition of the
control buffer that you use to disrupt binding? Is it denaturing or a mild
condition?
If the Rmax=150 and Koff=1e-6, then at 7200 s (2 hr), the signal will only drop
1RU from 150RU (assuming you can reach
Hi Xianchi,
First of all: a very slow dissociation rate can also be an artifact: the
analyte can be simply precipitating on the surface. You do need to rule this
out by proper controls.
But there is no rule saying that 10e-6 s-1 off rate is not realistic. Even with
protein-small molecule bind
Hi Jacob,
Interesting topic.
This reminds me the posters I saw on ACA 2010, on the femto-second infrared
laser based instrument . That instrument utilizes the nonlinear optical
properties of crystals of chiral molecules to detect very small crystalline
materials from amorphous background: the
: A K
Sent: Wednesday, February 13, 2013 6:51 PM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] GeForce Graphics cards
Hi Zhijie,
thanks for the link. I was actually referring to that post. Can you please tell
me what graphics card you are using?
Alex
On Wed, Feb 13, 2013 at
Hi Alex,
The graphical computational power of even the lowest-end graphic chips these
days will suffice the displaying of our models. To give you some idea: we
are still using a Quadro FX 1000 card and an old CRT on one of our stereo
systems; my 6-year old laptop has an ATI Radeon X1300, which
Hi,
Since it is mentioned, I would like to take this chance to clarify:
We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a VM
Windows within a Linux system, on either desktop (with a minimal on-board
graphic chip) or laptops. The monitor is quite plug-and-play in all case
Hi Sabine,
We are absolutely happy with our LG D2342P. The major advantages include the
simplicity in setting up and the light weight of the glasses.
For more information, please read this thread:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27816.html
Zhijie
--
Hi,
Seems not officially retracted from Nature either. On the paper's web page,
there was only a line in small font read like this:
There is a Brief Communications Arising (9 August 2007) associated with this
document.
It took me more than half an hour to find this line. I normally won't rea
Hi Wenhe,
Superpose allows you to specify residue (as well as Ca/main chain/side chain)
ranges. Also in COOT you can select the range of residues used in the LSQ
superpose calculation.
For superposing parts of the proteins only, a little trick is to cut the
interested fragments from the origi
UMAS Philippe (UDS)"
Sent: Friday, October 19, 2012 6:15 AM
To: "Zhijie Li"
Subject: Re: [ccp4bb] PNAS on fraud
Le Jeudi 18 Octobre 2012 22:52 CEST, Zhijie Li a
écrit:
Thank you for this funny (and yet significant) comment.
But I do not see clearly whether you agree with me
On curve fitting:
http://twitpic.com/8jd081
--
From: "DUMAS Philippe (UDS)"
Sent: Thursday, October 18, 2012 1:52 PM
To:
Subject: Re: [ccp4bb] PNAS on fraud
Le Jeudi 18 Octobre 2012 19:16 CEST, "Bernhard Rupp (Hofkristallrat a.D.)"
a écrit:
are quite established for the specific
proteins. I suppose that supports the idea that it at the minimum does not
always cause problems.
Zhijie
From: Rashmi Panigrahi
Sent: Thursday, September 20, 2012 8:29 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] sarkosyl
Thanks Zhij
Hi,
We used it in some lysis/refolding buffers.
Sigma marked this biodegradable detergent as "Highly toxic by inhalation" -
when it's used in toothpastes and shampoos if I am not mistaken. when I
called, Sigma said that since someone published a paper saying that when they
sprayed it into a r
P.S.
If the images are important and you want to extract them as independent image
files, then you can try saving the PDF as html. Acrobat will generate an image
directory that contains the image files. I am using acrobat 8 and there are two
options, saving as html 3.2 and saving as html 4 with
If you have acrobat (instead of acrobat reader), then you can save PDF to RTF
file which is fully supported by word. This is probably the easiest way to get
the maximum out of a PDF file. If this doesn't work to your satisfaction, then
you can try saving the PDF to TIFF images, then OCR.
From
stant Professor
University of Maryland
IBBR/CBMG
Rm 3127E CARB-2
9600 Gudelsky Drive
Rockville, MD 20850
email: swals...@umd.edu
phone: (240) 314-6478
fax: (240) 314-6255
On Aug 9, 2012, at 2:26 PM, Zhijie Li wrote:
Hello,
We have received our LG D2342P-PN monitor yesterday and did a little
ar Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
On Jul 23, 2012, at 11:42 AM, Zhijie Li wrote:
Dear CCP4BBers:
Sorry to bring up this highly repeated topic again. After some internet
research, we are about to make the commitment to
Dear CCP4BBers:
Sorry to bring up this highly repeated topic again. After some internet
research, we are about to make the commitment to buy an LG D2342P-PN for
setting up a stereo system. I would like to have a final confirmation from
someone with real life experience that this model does work
RE: [ccp4bb] harvesting in cold roomDensity of LN2=807g/L, that's roughly
807/28*22.4=645.6L gas at RT, 1 atm. At 4C the volume will be less:
645.6/298*277=600L. An empty 2x2x2m cold room=8000L, containing 8000x21%=1680L
oxygen.
We normally won't let the whole liter of LN2 to evaporate when fre
Hi,
Yes, it can be done by yourself. I repacked our 26/60 column a few years ago
with homemade apparatus. The column has been working for us since then.
Basically the loading apparatus was a tubing connecting the top of the
column and bottom of a reservoir (a flask with an opening near the bot
Hi Jun,
In this following article an metallic adapter was used to mount a 192 well
sitting drop plate on a conventional thermocycler.
http://journals.iucr.org/d/issues/2006/05/00/av5047/av5047bdy.html.
However I guess there would be significant evaporation and condensation if you
use vapor diff
Hi Fengjuan,
It has been proposed that for a specific protein there are "hard precipitants"
and "soft precipitants". Hard ones precipitates the the protein effectively,
while soft ones may help stabilizing the protein. By playing with the two types
of precipitants, one may get better crystalliz
Hi,
The idea used by the Qiagen pre-screen might be relevant to your case:
http://www.qiagen.com/products/protein/crystallization/screeningproteincrystallizationconditions/prescreenassay.aspx
http://www.qiagen.com/literature/handbooks/literature.aspx?id=239
Zhijie
From: fengjuanlv12
Sent:
I am little curious about the anisotropically truncated data for 3RKO:
Percent Possible(All)96.0
Mean I Over Sigma(Observed) 0.8
In the supplementary table of the nature paper it was made clear that this
3.16-3.0A, I/sigmaI=0.8 and Rmerge=1.216 shell was the outer shell of the
a
Hi Gloria,
I asked for a little baker's yeast from a lab in our department and PCRed
both the SMT3 domain and the SUMOase gene from its genomic DNA, then cloned
them to E coli vectors. The good thing about yeast is that most of its genes
are single exon so one do not really need to find cDNA f
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