Hi Chen,
I used SUPPOSE previously. It worked very well. The compositions of the
structures have to be the same! It works on Linux.
http://structbio.vanderbilt.edu/~jsmith/suppose/
If the compositions of your structures are different, you may first load
them to PyMOL, then align them use its com
Dear all,
I am just wondering whether there is a simple command line tool for RMSD
calculation between two aligned structures? I just cannot find a good
answer online, and ccp4bb can always impress me.
Thank you so much in advance,
Chen
Again, I appreciate all of your suggestions. I have tried many of them and I am
excited to report that I have had great success with the Crank-2 Enhanced EP
pipeline in ccp4 as recommended by Navraj Pannu. Even without my partial
rosetta model, Crank2 was able to build a model that covers ~85% o
An alternative is to dissolve your compound in MeOH and dispense it either
manually or via robot, let the plate sit sometime in the hood for faster
evaporation and then add your protein + reservoir.
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Hea
Thank all of you for your inspiring information! Now I understand that
actually axis order permutation and phase flipping can have the same effect
on the map.
All the best,
Steven
On Wed, Oct 15, 2014 at 4:48 AM, Ian Tickle wrote:
> The signs of the phases will depend on the permutation order
Since you mentioned EtOH, why not do this:
-Make a tray with the appropriate mother liquors
-Make a drop for each well containing mother liquor and high-concentration
ligand in EtOH (you could vary the ratios here as needed.)
-Equilibrate by vapor diffusion until EtOH all goes into the well soln
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Brief comment based on single experiment with the CHO-Lec-:
In principle the cells are compromised, so expect lower yields, but a single
N-clyc site might be a good omen.
In our hands with 5 sites on 70 kDa, the patterns had clearly reduced but still
significant complexity
per MS/HPLC glycan
Monica,
I struggled with this a lot too. I had some success with low molecular
weight PEG (100-400) as a solvent, its well worth a try.
-bob
On Wed, Oct 15, 2014 at 9:13 AM, Monica Mittal
wrote:
> Dear All
>
> Can anyone give suggestions for handling the solubility problem of
> highly hydrophob
Dear Alisa,
Thank you for your suggestions. The carbohydrate should be N-linked and the
protein was expressed in HEK293 cells. Chances of getting another protein
batch in the short-term are slim, so I am looking for ways to trim existing
carbohydrate chains. I will look into PNGase F.
Best,
H
Depending on how you produce the protein you might want to try CHO-Lec
cells which are only able to produce the high mannose core structures
of N-glycans as they lack further transferases. Further treatment with
Endo H leaves only the reducing end mannose of the N-glycan chains.
Some other
Dear Herman,
You did not specify the site of glycan attachment (is it N- or O-lonked?).
I assume it is N-linked as your carbohydrate is quite large. And what
expression system are you using?
In general you can first try PNGase F, however if you are unlucky it will
only cleave in the presence of SD
Yes, this is tough. We mostly have used DMSO or DMF. You can try detergents,
but they tend not to be that effective in solubilisation and they might bind to
your protein rather than the compound you 'd like to bind. If you'd like to be
adventurous you could try using cyclodextrins as a solubili
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Dear Herman,
Assuming that the protein is eukaryotic, and glycans N-linked, various ways of
dealing with the issue are described in PMID: 17355862.
Best wishes,
radu
--
A. Radu Aricescu, PhD
MRC Senior Research Fellow
Associate Professor
University of
Dear All
Can anyone give suggestions for handling the solubility problem of
highly hydrophobic compounds, during co-crystallization or inhibition
assays?
The ligands I am using are almost insoluble in aquous medium. In DMSO
or 95% Ethanol, the solubility is higher.
Besides crystallization, this so
Dear Bulletin Board,
I am struggling with a protein domain of 15 kDa, with about 22 kDa carbohydrate
attached. So far, the domain did not crystallize and I suspect the carbohydrate
may hinder crystallization. Completely removing the carbohydrate results in low
expression yields and poorly solub
I know this has not much to do with crystallography, but I think it’s worth the
time reading and deciding if you want to watch the webcast that took place
yesterday at Johns Hopkins School of Public Health.
http://www.jhsph.edu/events/2014/ebola-forum/
http://www.jhsph.edu/events/2014/ebola-for
Dear Sanjit,
use the BD with lots of grains of salt and verify with a real experiment that
the found binding pocket is real, else this is waste of money.
If you know of a known ligand to interact with your particular protein, you can
use this as a test BUT depending what your input model is e.g.
You need to specify the cell for the map.
This can be done by editing the CRYST1 card in the pdb header - presumably
to be 307.2 307.2 307.2 etc..
If that is done and tou use grid 128 128 128 that is another way to get the
desired pixcel size
Eleanor
On 15 October 2014 10:22, Kevin Cowtan wrote:
I'm not sure, but I think you'll have to do a 'run and edit command file'
and add the following keyword:
GRID SPACING 2.4 2.4 2.4
Give it a try.
On 14 October 2014 17:31, Steven Chou wrote:
> Dear All,
> I'm trying to generate a mask from a pdb coordinate file using the
> 'Ncsmask' utility of C
Dear All
I wish to know If the experimental determination of
ligand-protein complex structures is difficult to analyze or if the
ligand protein complex structure is not known. Then blind docking (BD)
and pocket search (PS) calculations would be good in the prediction of
binding mode and
The signs of the phases will depend on the permutation order of the axes.
Maybe when you created the map you inadvertently reversed the hand? What
do you see if you run mapdump on the map?
Cheers
-- Ian
On 15 October 2014 01:53, Steven Chou wrote:
> Dear All,
>
> I used 'sftools (in CCP4)' to
Dear Gabriel,
since you are already using autoSHARP: why not giving it the MR model
as input too? This way you will combine the model and the experimental
phasing.
This combination can not only be done in autoSHARP (for SAD, MAD,
SIR(AS) and MIR(AS)), but also in SHARP directly for any phasing
sc
Dear All,
Can someone sugegst what would be the best options for stereo viewing for macs
currently?
Any good experiences with Stereo-TVs? Other? I would like know the specific
combination (at least
which mac computer etc) if possible to find out something that works.
Thanks,
Tommi
Tommi Kajan
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