Dear all,
Before we try to study the crystal structure of an unknown protein, we
need to determine the sequence that can fold into a compact and stable 3D
domain. What kinds of methods can we choose?
--
Best regards,
XH Wu
Hi,
There's a whole bunch of programs that can help you out there.
The 2 methods I think of right now are DISPROT (there's a server I
believe, http://www.ist.temple.edu/disprot/ ) - Must admit I haven't
been to that one for quite a while; DISPROT provides areas of your
sequence with high
Dear all,
Sorry for this slightly off-topic email, but I am looking for a
transparent sealing tape for 96-well crystallization plates, with the
following properties:
- high sealing performances
- compatible with UV screening
- optionally, available as rolls
Thanks for your help
JL
--
Jean-Luc
Hi Jean-Luc,
We have complied a list of UV compatible cover media and plates. The
list is by all means not complete yet, but the best seals we found are
all sheets (that does not mean all sheets are UV compatible!). If you
want I can send you a PDF file outside of the BB.
Flip
On 3/7/2011
Hello everyone,
Thank you very much for giving me such a valuable information. I will try one
by
one each suggestion and then ask again if i feel more problem.
thanks regards
Sadaf Iqbal
PhD Scholar
ICCBS, University of Karachi, Pakistan.
Visiting Scientist
University of Hamburg,
I have to say that I don't fully agree with James' recommendation to
adjust the GAIN in MOSFLM until the calculated SDFAC parameter in
SCALA is 1.0.
(Background information, the sigmas from Mosflm sd(I) are corrected in
SCALA according to
sd(I) corrected = SdFac * sqrt{sd(I)**2 +
Hi Sadaf
It is also possible that the features you observe are also due to anisotropy of
the ADPs. At 1.3A resolution you can perform anisotropic refinement. Give it a
go and se if it helps.
Best
Roberto
On 6 Mar 2011, at 18:57, sadaf iqbal wrote:
Hello everyone,
Recently, i have solved a
hello Bert
u can also add 50mM to 100 mM Argine and glutamate either alone or
combined together..it really works fine..although it will increase the
protein stability many fold but i dont know whether it will impede
crystallization or not..
others comments are welcome..
Faisal
SLS, JNU
New
Hi Tom--
We have had good luck crystallizing proteins with 5-10% glycerol. In the
majority of these cases, the glycerol was included in the buffer for the final
purification step. We have also seen several cases where 1,2-propanediol
worked much better than glycerol.
Hope this helps!
annie
hello everybody
how does arginine and glutamate affect crystallization..what will be
the better stabilizing agent during protein purification which wont
affect crystallization or have minimal affect on
crystallization..example..glycerol, sorbitol, glycine, poline,
arginine, glutamate..what should
It seems that your mtz doesn't have the map coefficients on it, that is why
it is failing. Check if it has the columns FWT PHWT.. If it doesn't them
coot will not automatically recognize it. A simple solution would be to run
a cycle of rigid body refinement in Refmac and use the output mtz as
Thanks for your suggestion. Your two suggestion is directing me go right to
the heart of the matter.Thank you again.
Best wishes
Wangrui
2011/3/7 Mario Sanches mario...@gmail.com
It seems that your mtz doesn't have the map coefficients on it, that is
why it is failing. Check if it has the
Please see below details of a software development post available at Diamond.
For full details please go to the web pages at:
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Dear All,
If you are planning to come to the British Crystallographic Association
Spring Meeting in Keele this year today (7th March) is your last chance
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You can register here:
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Hello,
I was trying to install PYMOL in my openSUSE 11.3 as follows:
cd /usr/local
hena@a:/usr/local
sudo svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymolpymol
cd pymol
hena@a:/usr/local/pymol
sudo python setup.py install
And I got the following error at the end:
package
Hello Hena,
I was trying to install PYMOL in my openSUSE 11.3 as follows:
...
In file included from modules/cealign/src/ccealignmodule.H:57:0,
from modules/cealign/src/ccealignmodule.cpp:32:
layer0/os_python.h:30:19: fatal error: Python.h: No such file or directory
You're
Hi,
If you're missing Python.h (since your compiler complains about it), I
guess you're missing the development package of python, whatever that's
called in SUSE. Probably python-devel, according to this:
http://www.novell.com/products/linuxpackages/opensuse/python-devel.html
Good luck,
Sorry for my earlier non CCP4 posting in CCP4BB.
hena
On Mon, Mar 7, 2011 at 9:30 AM, Ben Eisenbraun b...@hkl.hms.harvard.eduwrote:
Hello Hena,
I was trying to install PYMOL in my openSUSE 11.3 as follows:
...
In file included from modules/cealign/src/ccealignmodule.H:57:0,
Hi,
To start with it would be great if you look in to the secondary structure
prediction of the sequence using any of the standard servers like PSIPRED,
JPRED etc. Many more available at expasy site http://ca.expasy.org/tools/.
Whatever construct you finally choose to make just remember the
for an experimental way to determine soluble domains see the following paper:
ESPRIT: an automated, library-based method for mapping and soluble expression
of protein domains from challenging targets.
Yumerefendi H, Tarendeau F, Mas PJ, Hart DJ.
J Struct Biol. 2010 Oct;172(1):66-74. Epub 2010 Mar
Hi,
I just installed CCP4-6.1.13 on my ubuntu (10.10) 64 -bit laptop. I can run
CCP4i successfully. But when i try to run coot, i get error : No command
'coot' found. Can someone help me to fix the problem?
with regards,
Pranjal
coot has to be installed separately, it is not included in ccp4 6.1.13. It is
best to get coot binaries from Paul Emsley directly, just google on coot
emsley and look for download pages, then choose ubuntu tarball.
Best,
Eugene.
On 7 Mar 2011, at 18:27, Pranjal Mahanta wrote:
Hi,
I just
I install this version of coot: coot-Linux-x86_64-ubuntu-9.04-gtk2 for
ubuntu and it works fine
Best
Lionel
Le 07/03/2011 19:35, Eugene Krissinel a écrit :
coot has to be installed separately, it is not included in ccp4
6.1.13. It is best to get coot binaries from Paul Emsley directly,
just
All,
Pardon the slightly off-topic question.
We would like to use Pymol and generate movies with it on a WINDOWS computer.
We are very familiar with Pymol and how to make the correct views etc. We write
the individual frames out into PNG files.
So what is left to do, is to stitch together
Hey Mark,
In Window PC, I used ImageReady, which comes with Photoshop.
see this:
http://sage.ucsc.edu/~wgscott/xtal/movie/making_movie.html
Alternatively, using Mac version of Pymol, you can easily make a movie and
save it in quick time format
see this:
sorry, this is the right link for the mac-pymol movie:
people.chem.umass.edu/jhardy/BMS2006Files/pymol%20morphing/PymolMorphingMovie.pdf
On Mon, Mar 7, 2011 at 2:07 PM, Matthew Chu linghonmatt...@gmail.comwrote:
Hey Mark,
In Window PC, I used ImageReady, which comes with Photoshop.
see
On Mon, Mar 7, 2011 at 1:21 PM, mjvdwo...@netscape.net wrote:
We have found videomach, which costs a very small amount of money to
obtain. Similarly, Adobe Premiere is affordable for an educational
institution. We don't mind paying, but before we go there, does anyone have
experience with
Hi Mark,
just use the Windows Movie Maker - it's easy to use and comes along with
Windows (or can be downloaded via microsoft.com). This will help you to
generate .wmv output files of any kind of video and / or picture files you
provide as input files. The best possible quality output format
Dear Mark,
I put together a post about creating a movie using PyMOL, eMovie (free) and
Adobe ImageReady CS2 to generate a Quicktime movie.
http://www.p212121.com/2009/03/24/easily-make-movie-pymol/
I hope that helps.
Take Care,
Sean
P212121
http://store.p212121.com/
Hi Mark (and Matthias),
I'm not sure if Windows Movie Maker is the same as (or maybe the predecessor to?)
Windows Live Movie Maker (http://explore.live.com/windows-live-movie-maker?os=other),
but this is what I used recently to string together a series of png images from pymol to make a wmv
I use ImageJ for this purpose. There is a flag for something like
'use virtual stacks' or 'use virtual memory' that I needed to prevent
crashing.
Nat
On Mon, Mar 7, 2011 at 5:30 PM, Sean Seaver s...@p212121.com wrote:
Dear Mark,
I put together a post about creating a movie using PyMOL,
VirtualDub is the (absolutely free) program of choice, I'd say.
Good luck,
Matthias
Am 07/03/2011 21:21, schrieb mjvdwo...@netscape.net:
All,
Pardon the slightly off-topic question.
We would like to use Pymol and generate movies with it on a WINDOWS
computer. We are very familiar with
Friends,
I would like to draw your attention to the announcement below.
Informal inquiries are welcome (directed to me) however actual applications
should be directed to the web site listed in the announcement (use
requisition number 003Y4 to find the position and apply).
Thank you for your
Dear colleagues,
A post-doctoral position will be opened at the IBS in Grenoble (see
below). I would be very grateful if you could forward the information
below to potential candidates.
Post-doc position at the Institut de Biologie Structurale, Grenoble, France
*Structural Biology of DNA
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