Definitely magnesium salt. I've seen it many times. But try to repeat it
anyway just to be safe.
Nian
On Sat, Dec 1, 2012 at 8:24 PM, Yibin Lin yyb...@gmail.com wrote:
Dear Folks,
I got some crystals at the conditions of 0.1M Lithium sulfate or 0.1 M
MgCl2, 0.1M Sodium citrate 3.5 or Sodium
Not sure it is what you need. I put an external screen to my laptop when I
use HKL2000 for remote collection.
Best,
Nian Huang, Ph.D.
On Sun, Nov 18, 2012 at 8:48 PM, 王瑞 wangrui...@gmail.com wrote:
OK,thank you all of you. I have installed one copy of HKL2000 on our
desktop computer
Hi Michael,
I would recommend an alternative
http://www.mitegen.com/products/micrort/micrort.shtml
Traditional capillary is a pain to handle, unless you have a rock sized
crystal.
Good luck,
Nian Huang
On Mon, Nov 12, 2012 at 11:13 AM, Michael Roberts
mrobert...@talktalk.netwrote:
Dear All,
I
python 2.6. A transition to 3.2 maybe a pain in future.
Nian Huang
On Fri, Oct 19, 2012 at 3:12 PM, Aksyuk, Anastasia (NIH/NIAMS) [F]
anastasia.aks...@nih.gov wrote:
Hello all,
Considering that many biologists come to the field with no background in
programming (like me) and want to learn
Or make it yourself if you got time.
Anal
Biochem.http://www.ncbi.nlm.nih.gov/pubmed?term=a%20syringe%20based%20gradient%20former#1994
Sep;221(2):397-400. A
syringe-based gradient former for linear and exponential gradients.
Shearer G
Hi,
Sometimes the forming of ice is due to the high humidity in the air. I
recommend to put a dehumidifier in the room or silicone gel in your camber.
Nian
On Tue, Apr 24, 2012 at 9:52 AM, Kelly Daughtry kellydaugh...@gmail.comwrote:
Is there room in the LN2 to plunge directly in, then
I don't model zero occupancy in my model. But can't the refinement programs
just treat those atoms with zero occupancy as missing atoms?
Nian Huang
On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen jubo...@jhsph.edu wrote:
really fascinating, bringing back the discussion for a repository
I have seen people only use robot to optimize their crystal and get
good diffraction (~2 A). If you keep having trouble, you can try this
method instead, even though generally the case is the bigger the drop
the bigger crystal.
I remember the archive suggest us to use higher concentration of
production in insect
cells.
But my request of plasmid (GenBank Accession No. DQ003705) to the
correspondent author got rejected by the email server. Is there any
other way to contact the author or request the plasmid?
Thank you very much.
Nian Huang, Ph.D.
Instructor,
MC 8816
UT Southwestern Medical Center
Is it possible the solution structure of SAXS, NMR and EM neglect the
existence of a very small percentage conformation of the molecule due to
the overwhelming signals from the majority conformations? But this state of
the molecule is trapped and enriched by the crystallization condition.
Nian
MolProbability score doesn't mean too much in your case, since you are
essentially using a 1.5 A model against a 3 A database. The differences in
the blobs might caused by the different delta sigma settings when you were
viewing these two models.
I have successfully used TLS for a 3 A dataset
Just a reminder. Quickchange is not PCR. It is linear amplification. It is
very hard to see a band in the gel if you follow the standard protocol.
Nian
On Fri, Feb 3, 2012 at 12:14 PM, Fred ccp4bb.l...@gmail.com wrote:
Hi CCP4 list,
Thanks everyone who have answered my post concerning to
of the lifted flap. (Apologies for the attachment).
hope your crystals go well.
Martyn
--
*From:* Nian Huang huangn...@gmail.com
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Tuesday, 15 November 2011, 17:44
*Subject:* Re: [ccp4bb] [off topic] Control of crystals' direction
Thank you guys. I basically tried almost everything that I can find in the
hampton catalogue and in this bulletin, seeding, hanging, sitting,
sandwitch drops (which made things worse), temperature, gel, oil batch, and
additive screens. Manipulating the crystal with fiber increases the chance
to
Hi,
I agree with other people. You must have a wrong index here. Can you tell us
what is the unit cell for this crystal from your determination? I can see
very close spots in the high resolution shell from your image, which are
overlapped into one spot in the low resolution shell. Try to use other
A dual boot laptop is all you need. I always reinstall the windows to get
rid of bloatware anyway. If you are going to buy a mac, you can also try the
triple boot, but I don't think anybody is doing it. Although it is very
convenient, a virtual machine will affect the performance of the software.
(or want!) a triple boot system? It all seems to work just fine on OS
X.
Tony.
On 30 Aug 2011, at 07:38, Nian Huang wrote:
A dual boot laptop is all you need. I always reinstall the windows to get
rid of bloatware anyway. If you are going to buy a mac, you can also try the
triple boot
a standard ran fine. That's why I suspected
the mixing of reagents in the column has something to do with it in
the beginning.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Sun, Aug 28, 2011 at 5:14 PM, David Briggs drdavidcbri...@gmail.com wrote:
Hi Nian,
It can be a number of things
Hi, David,
What is the common cause of knackered SEC column? Will equilibrizing a
buffer containing 150 mM NaCl directly into a 20% EtOH or vise versa cause
the problem. There was no problem just after packing the column.
Nian
On Sun, Aug 28, 2011 at 9:24 AM, David Briggs
To make my idea a little bit clearer, the reviewers first make the
acceptance decision just based on the paper itself, on the condition the
coordinate matches the description of the paper. Then the editor promises
the publication date and the pdb can be subjected to final quick review,
either by
I Agree with the idea of adding crystallographer reviewers. But accessing to
data is not feasible unless there is a good way to protect authors. For
example, the editor should agree to publish the paper swiftly in advance
before the data become accessible to reviewers.
In any case, the flaw of
The R and Rfree are low enough so your space group is correct. I don't see a
resolution in the log file. If it is 3 A dataset, 28% is not bad for a start
at all. The N terminal region is probably completely disordered if it is not
degraded.
Nian
On Sat, Jul 16, 2011 at 3:47 AM, Appu kumar
It might be SDS precipitation. Although 0.1% SDS is generally considered not
high enough to precipitate at 4 degree, it might interact with other
components in your solution to form even less soluble material.
Nian
On Fri, May 20, 2011 at 9:36 AM, WEI MIN butiany...@gmail.com wrote:
Dear All
Check pymolwiki for the full description of setup. It should work for coot
too.
http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options
Nian
On Fri, May 6, 2011 at 10:27 AM, zhang yu ccp4f...@gmail.com wrote:
Dear colleagues,
Sorry to present the stereo issue to the board again.
Since
disulphides (bad: aggregates) while
at the same time preserve the valuable intra-molecular ones (good:
structure)
Artem
On Sat, Apr 16, 2011 at 11:46 PM, Nian Huang huangn...@gmail.com wrote:
Dear Horacio,
How does TECEP compare to BME or DTT? People claim it is better, but I
want some
Dear Horacio,
How does TECEP compare to BME or DTT? People claim it is better, but I want
some crystallographers' opinion?
Nian
On Sat, Apr 16, 2011 at 4:24 PM, Horacio Botti hbo...@pasteur.edu.uywrote:
Dear Mike
BME readily autooxidizes (need for metal traces and dissolved O2). Is yours
a
Heparin simulates the structure of DNA and RNA, so it has nonspecific
affinity towards DNA or RNA binding protein. It has also been used as DNAse
or RNase inhibitor but it is not very good one.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Sat, Apr 9, 2011 at 7:44 PM, Alexandra Deaconescu
and
thrombin with rocking or shaking. The important part is that you have to
have good protease to start with.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Thu, Mar 31, 2011 at 2:41 PM, gauri misra kamga...@gmail.com wrote:
Just an offshoot of the same Question..
I would like to ask whether
Superdex 200 instruction manual suggests a minimal 150mM NaCl is
required to prevent binding of protein to the resin. But it seems more
to the side of preventing loss of protein instead of misjudging
protein size.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Tue, Mar 22, 2011 at 7:23 PM
shuttle glass though). You can easily
retrieve the Nvidia driver from the repository if Ubuntu hasn't
already done it for you. But the bad side is that you are going lose
your computation skill since you have less problem to handle.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Tue, Feb 22
I'm downloading ubuntu - is that a good choice? Can I run different
flavors of linux with nfs and share drives in a local network (so one
has fc7, one has fc13, and another has ubuntu)?
Replied too fast and didn't finish your message. I have Ubuntu and
most of other machines in NFS are running
Mitegen plastic capillaries can actually last about a week from a
Mitegen seminar I attended. I also got ice when I tried to freeze it
once and I didn't further pursue it. Maybe coat the capillary with
glycerol will help?
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Thu, Feb 17, 2011
That's great. The 3D screen we got is only 23 inch. A full screen GUI
like in the game will certainly be helpful.
Nian Huang, Ph.D.
Dept of Biochemistry
UT Southwestern Medical Center
Dallas, TX 75390
On Fri, Dec 31, 2010 at 5:00 PM, Nian Huang huangn...@gmail.com wrote:
Dear all,
The python
.
Nian Huang, Ph.D.
Dept of Biochemistry
UT Southwestern Medical Center
Dallas, TX 75390
Definitely small molecule crystals. You might want to push the
detector closer and use better cryo solution for further confirmation.
Nian
On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang congru...@gmail.com wrote:
Dear Colleagues,
Currently we got several very tiny crystals. After exposuring
Try this, assuming you have good data. Use one molecule you got to do
refinement (rigid body or restraint refinement with tight restraint)
and phase the map. Then do a phased map molecular replacement. You
might want only use the core of your protein to do the molecular
replacement search to
a hydrophobic column after treating the protein
with really high salt. The last one worked for one of my colleagues.
Although I still doubt you can completely get rid of the ligands.
Nian Huang, Ph,D.
Dept. of Biochemistry
UT Southwestern Medical Center
Dallas, TX 75390
On Thu, Oct 7, 2010 at 8:05 PM
Hi, Salameh,
As Pavel said, you might have a ligand with incorrect cif file. A
quick fix is to run phenix.elbow on that cif file, which worked for
me. I will try the new version of phenix and to see if it can fix the
problem. Hopefully you already solved the problem.
Nian Huang, Ph.D.
UT
. So the default has tighter weight
than your specification. Just use default setting instead.
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Fri, Mar 12, 2010 at 11:59 AM, Salameh, Mohd A., Ph.D.
salameh.m...@mayo.edu wrote:
Yes Im using wxc_scale and wxu_scale but I also use tls refinement
/medialib/en/filelibrary/pdf.Par.99253.File.dat/O-063575-NuPage_fin.pdf.
The Bis-Tris/Mes gel can resolve 2.5KDa peptide.
Regards,
Nian Huang, Ph.D.
Univ. of Texas Southwestern Medical Center
On Thu, Feb 11, 2010 at 1:13 PM, Jacob Keller
j-kell...@md.northwestern.edu wrote:
Dear Crystallographers
Deleting the loop /unessential regions is a more robust way to go. You
will be surprise to see that how much those regions can contribute the
clashes. Increasing clash tolerance in Phaser makes the program runs
really slow and gives ambiguous results.
Best,
Nian
On Wed, Oct 21, 2009 at 11:41
Hi, Kevin,
Wash your crystal very very well to get rid of unbound DNA. Then run
your crystal with SDS PAGE gel, with protein and DNA as markers. After
staining the gel with silver stain, the DNA will show with different
color and migrate about where the dye locates. So don't run too long
time.
Hi, Amit
If you mostly got clear drops, you might first increase your protein's
concentration before you try anything else. Of course, I assume you
have a lot of protein, since you are think about doing lysine
methylation.
Best,
Nian
On Wed, Jun 10, 2009 at 6:24 AM, amit sharma3112a...@gmail.com
You always get the entry of Bromide into crystal by quick soaking,
because it does not require the incorporation of Bromide into the
protein. But whether the signal is good enough for phasing is another
story. You have to collect the full data set to know the answer.
Nian
2009/3/31 tat cheung
You can try TOPS.
http://www.tops.leeds.ac.uk/
Best,
Nian
On Fri, Aug 22, 2008 at 8:57 AM, Buz Barstow [EMAIL PROTECTED] wrote:
Dear All,
Does anyone know of a program that is capable of drawing the secondary
structure of a protein molecule?
I'd really like to be able to take a protein
It should be straight forward. A good example you can use is to make
an alternate conformation of a residue in coot. Then you can follow
the generated pdb to modify your ligand. Are you sure refmac won't
run? What is the error message from refmac?
Nian Huang, Ph.D.
Dept. of Biochemistry
UT
I will try that. But I don't think people can tell the final
concentration of glutaraldehyde in the drop by using its vapor. Maybe
using direct soaking is what I should do. By the way, should I quench
it by ammonium or not?
Nian Huang
Dept of Biochemistry
UT Southwestern Medical Center
Dallas, TX
. I am just wondering what will happen
if I use some other crosslinking chemicals.
Nian Huang
Dept of Biochemistry
UT Southwestern Medical Center
Dallas, TX 75390
On Sun, Mar 2, 2008 at 12:28 AM, Nian Huang [EMAIL PROTECTED] wrote:
Dear all,
I know most people use glutaraldehyde
they compared with glutaradehyde? I have a crystal very sensitive
to glutaradehyde but I really wants to try the crosslinking method.
Thanks,
Nian Huang
Dept of Biochemistry
UT Southwestern Medical Center
Dallas, TX 75390
Dear All,
I have been trying to get a protein-ligand complex crystal for a long
time. Here, ligand is either substrate or product for this kinase. I
have tried many methods: soaking with apo-crystal, co-crystal with
different concentration of ligand and screen for new conditions. I got
a couple
Hi, all,
I met some crystal structures with disordered active sites. Soaking
common ligands can not make it become ordered. I am wondering what
people generally do in such situation.
Thanks,
Nian Huang
WOW. There are so many ways to do it. Thank you all for replying.
Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center
On 5/10/07, Charlie Bond [EMAIL PROTECTED] wrote:
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g
Dear all,
I was trying to do a NCS averaging of the map using Resolve. I had a
partial model, which generated a rotation and translation matrix by
program lsqkab. Resolve also requires a center of mass input. Do you
know any program can estimate it either by map or pdb file?
Thanks.
Nian Huang
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