Hi Mark,
What about UCSF Chimera? Very easy to use.
http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
More on the topic:
http://www.cgl.ucsf.edu/chimera/animations/animations.html
Check out the Nuclear pores movie. Amazing stuff. A few years back one had to
pay huge $$$ for
Dear Mark,
I am always using mencoder with Windows and it has so far always worked
fine for me.
I didn't need to install anything, normally I just copy the mencoder.exe
file to the directory with my png frames.
Then, I use the following command line in a DOS command window:
There is a vacancy for a software developer at the University of Oulu.
Details are below, and also at:
http://www.oulu.fi/dokumentit/jobs/xtalPiMS_Software_Developer.rtf
regards,
Chris
Chris Morris
chris.mor...@stfc.ac.uk
Tel: +44 (0)1925
Thanks for your kind help. i am able to fix the problem. I installed
coot-Linux-x86_64-ubuntu-9.04-gtk2 and set the path variable. now it is
working fine.
thanks again,
Pranjal
On Tue, Mar 8, 2011 at 12:10 AM, Lionel Cladière cladi...@sb-roscoff.frwrote:
I install this version of coot:
Dear all,
I was wondering if somebody could help me out by suggesting the best column
to be used in a Static Light Scattering (I guess it would be the same for a
Multi Angle Light Scattering) instrument.
We were suggested using a silica-based column, with very high separation
properties, but it
Posted on behalf of Prof Neil Fairweather:
Post-doc in Structural Biology of Bacterial Pathogens
Imperial College London
A post-doctoral research associate with experience in crystallography is
available in the laboratory of Prof Neil Fairweather.
The position, funded by the MRC, is to
Dear CCP4-ers,
_
Postdoctoral position in reactive oxygen species (ROS) biology
A postdoctoral position supported by the King’s College London British Heart
Foundation Centre of Excellence is available at King’s College London in the
field of
* MRC Laboratory of Molecular Biology *
We are looking for a postdoctoral scientist with a computational
background to join the group of Sjors Scheres on the development of new
statistical image processing approaches, such as maximum likelihood
refinement, for cryo-electron microscopy. Our
Also, consider this
http://www.mail-archive.com/coot@jiscmail.ac.uk/msg02024.html
On Mon, 2011-03-07 at 23:57 +0530, Pranjal Mahanta wrote:
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
Dear Sebastiano,
From my experiences, Wyatt columns are the best.
Best wishes,
Sally.
On Tue, Mar 8, 2011 at 2:03 PM, Sebastiano Pasqualato
sebastiano.pasqual...@gmail.com wrote:
Dear all,
I was wondering if somebody could help me out by suggesting the best column
to be used in a Static
Hi Sebastiano,
we are very happy with the SEC columns from Wyatt coupled to our FPLC/MALLS
machine.
http://www.wyatt.com/solutions/hardware/sec-columns-for-multi-angle-light-sc
attering.html
The separation range is (more or less) comparable to GE standard spdx
200/75/superose 6, and the columns
Hey Mark,
You could also try the MPEGstreamclip for windows: http://www.squared5.com/.
This would read .png files and put them together in a variety of supported
formats.
-Caroline
On Mon, Mar 7, 2011 at 10:21 PM, mjvdwo...@netscape.net wrote:
All,
Pardon the slightly off-topic question.
Hi Sebastiano,
we have used both silica based and superdex columns and we found the
second as a better option for general usage.
Most of our proteins are on basic buffer and about 50% of them stick on
the silica based column. On the other side a superdex 200 10/30 from GE
performed quite
I should say clearer that I did a comparison between GE (Superdex 200
10/30) and the Wyatt column of the same separation range on AKTA
connected with MALS. The Wyatt column gave better resolution for size
exclusion chromatography as well as signal-noise ratio for light
scattering. So I think it
So from where does Wyatt outsource their columns?
JPK
On Tue, Mar 8, 2011 at 10:49 AM, Sally Pham Thanh Van
sally.pha...@gmail.com wrote:
I should say clearer that I did a comparison between GE (Superdex 200
10/30) and the Wyatt column of the same separation range on AKTA
connected with
Hi,
they buy it from some small company, idea being the applicability to
SLS, optimized for minimized bleeding/sheding or material
from the column, which will show up only in the light scattering
detector.
but i have to say some of our proteins stick to their columns
(happened during the
On 3/8/11 5:03 AM, Sebastiano Pasqualato wrote:
On the other hand, GE Healthcare columns would require a huge amount of
material to be loaded.
What do you mean by a huge amount of material? You would not be using a
16/60 column (125 ml column volume) for an analytical experiment. How
about a
they buy it from some small company, idea being the applicability to
SLS, optimized for minimized bleeding/sheding or material
from the column, which will show up only in the light scattering
detector.
I don't know. Every single spec of Wyatts columns looks exactly the same as
Bio SEC-5 series
And as others have said shedding of dextran is a problem with GE columns
(this was confirmed to me by GE people), but after extensive system
equilibration, we do not see a problem significant enough to ever hurt
our light scattering measurements.
Engin
On 3/8/11 10:38 AM, Engin Özkan wrote:
Although George does not mention anything about data reduction programs,
I take from his description that common small-molecule data processing
packages (SAINT, others?), have also been modernized to record all data
(no I/sigmaI 2 or 3 cutoff). I agree with him that this is a good
thing!
Andrew! You don't believe me? Well, I suppose it serves me right for
not explaining where the idea came from (see below).
I do, however, agree with Andrew's assessment that the default-chosen
gain in MOSFLM is adequate for all practical purposes. Any error in
GAIN will be almost exactly
Hello all,
For any given structure in the PDB, I want to identify all the Histidine ND1
atoms. I then want to consider these atoms in pairs, measure the distance
in Angstroms between the ND1 atoms in each pair, and compile these distances
(along with residue numbers of the pair) in a table. I
On Tue, 2011-03-08 at 17:44 -0500, Cale Dakwar wrote:
Amongst other things, I want e.g. generate a histogram from this table
and determine e.g. the shortest HisND1 pair distance observed and the
structure in which this happens.
For this specific question this can be useful
Hi there,
I am trying to build the LINK information in PDB header for
sugar-containing protein, and I am wondering whether there is some utility
in CCP4 (or any others) can do it automatically (eg by measuring
inter-sugar distances). Thanks in advance!
Best Regards, Hailiang
Thanks for the quick reply. This is a very good resource but not quite what
I need. As far as I can tell, this resource is based on a dataset from
10-08-1998 and then only included x-ray crystal structure with better than 2
angstrom data. I also can't in this database a mention of the PDB
Hi Cale,
My advice would be to find someone local with experience in scripting
possibly in python or perl. This is a tractable problem with a bit of
scripting and if you aren't already experienced this may be a good
opportunity to delve into a bit of programing.
Good Luck,
-bob
On Tue, Mar 8,
Hello Bob,
I am familiar a little with scripting but was hoping someone knew of an
already existing tool. Alright, its off to perl then.
Thanks,
-c
On Tue, Mar 8, 2011 at 7:28 PM, Robert Immormino immorm...@gmail.comwrote:
Hi Cale,
My advice would be to find someone local with experience
On 3/8/11 5:44 PM, Cale Dakwar wrote:
Hello all,
For any given structure in the PDB, I want to identify all the
Histidine ND1 atoms. I then want to consider these atoms in pairs,
measure the distance in Angstroms between the ND1 atoms in each pair,
and compile these distances (along with
Hi Cale,
For any given structure in the PDB, I want to identify all the Histidine ND1
atoms. I then want to consider these atoms in pairs, measure the distance
in Angstroms between the ND1 atoms in each pair, and compile these distances
(along with residue numbers of the pair) in a table. I
Dear all,
I wonder if there is anyone who ever tried composite omit map with low
resolution data.
Is there any resolution limit for the composite omit map? or any criteria
could help deciding the practicability, like quality of data, map or
resolution?
I have ~3.7A resolution data and MR
Jason, that was pretty fast! You delivered the script before someone
else could even suggest PyMOL ;)
If you use
from chempy import cpv
cpv.distance(aa.coord, bb.coord)
instead of
cmd.get_distance( index %s % aa.index, index %s % bb.index)
it will be significantly faster.
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