dear colleagues,
i just noticed a to me somewhat unexpected behaviour of pdbset.
as it turns out, it seems to make a difference whether i do run pdbset
all in one go, changing the cell and applying transformations at once:
pdbset XYZIN ... << eof-pdbset
cell
spacegroup ...
rotate euler
shif
Dear all;
I am a fresher of Refmac5. And now I'm trying to refine a protein and labelled
RNA complex using Refmac. It's a Iodo-U labelled RNA. Unfortunately, these is
no appropriate lib file in the current refmac dictionaries. So I use cif file
which created by Refmc itself, surprisingly, the b
Dear all;
I am a fresher of Refmac5. And now I'm trying to refine a protein and labelled
RNA complex using Refmac. It's a Iodo-U labelled RNA. Unfortunately, these is
no appropriate lib file in the current refmac dictionaries. So I use cif file
which created by Refmc itself, surprisingly, the b
Hi,
In addition to the tips already suggested, you could also try to elute
your protein with histidine.. I've got a protein that crashes out with
imidazole as well, and I have succesfully used 200mM histidine for
elution (using either KPi or MES buffer in my case).
Cheers,
Ronnie
On Feb
Hi,
It's much easier to begin with the cif file created by Refmac5
itself, but this cif file needs to be checked and corrected
manually for the restrains. Certainly, Iodine is not happy
with the current restrains.
Most of the time, i have found problems beginning with the
protonation and th
Hi Florian,m
the keyword is TRUSTED_REGION (see
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#TRUSTED_REGION=
and http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS.INP
in XDSwiki).
HTH,
Kay
Florian Schmitzberger schrieb:
Dear All,
Is there a way
Dear All,
Is there a way to get XDS to include reflections in the far corners
of diffraction images.
XDS seems to take the high-resolution limit automatically from the
edge of the images corresponding to the smallest radius from the
center. In my case, with the keyword set to
"INCLUDE_R
Hi,
I used another way to deal with this problem. You can try to elute your
protein with the buffer containing 50mM EDTA (You need at least 10CV to
elute completely). Then use gel filtration to remove the Ni.
I applied this method with two proteins and it showed good results.
Good luck!
TriNgo
--
I have a crystal that grows with multiple lattices despite the fact
that the crystals look more or less like single crystals under the
microscope.
With a lot of guesswork I am able to index with mosflm by carefully
selecting spots that appear to be in the same lattice.
Now I would like to u
On Mon, Feb 18, 2008 at 01:58:59PM +0100, Jason Greenwald wrote:
> I have a crystal that grows with multiple lattices despite the fact
> that the crystals look more or less like single crystals under the
> microscope.
>
> With a lot of guesswork I am able to index with mosflm by carefully
>
Hmm...
Thinking about this it may not be too hard to do with XDS. May involve a
certain amount of fiddling though.
If you do the first stages of XDS processing, namely XYCORR, INIT,
COLSPOT & IDXREF you will end up with a spot file (SPOT.XDS) from
colspot and with indices attached from IDXREF. On
Hi,
One has to bear in mind that adsorption at high pH (above 6.5 is already
high for Imac; pKa of exposed His is 6.2) leads to stronger interactions
which, in turn, require stronger eluting conditions, e.g. > 200 mM
imidazole (pKa ~ 7.0).
I suggest lowering the pH of the adsortion buffer, e.g
Ok, Graeme basically described the way I usually do things as
well. That's the beauty of a modular program like XDS and the passing
of information in ASCII format. Old-fashioned, but very, very useful
;-)
I've created a short page with a recipe for using XDS in that way -
there might be some typos
Is there any way to do a search of crystal orientation matrices with a known
cell to find the best fit to the diffraction pattern? The data were collected
on the Pilatus6M detector so I am limited to mosflm and XDS for processing.
d*TREK will easily process Pilatus6M images.
Both packages alwa
I'm not sure if it will still work with the latest Mosflm/HKL, but
Untangle might also be worth looking into:
http://ultr23.vub.ac.be/untangle/
Luca
Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Hälsov
Hi,
I am using PISA to calculate the surface interface of a homdimeric
protein. Does anyone know where I can find the parameters (probe radius,
atomic radii, etc) PISA uses to calculate surface area?
Cheers,
Rafael.
Hi all,
We are preparing to replace a cryosystem on our home rotating anode.
Does anyone have any insight into a comparison of the Oxford Cobra
system and the Rigaku X-treme?
Many thanks,
Marilyn Yoder
Marilyn D. Yoder
Division of Cell Biology & Biophysics
School of Biological Sciences
Univer
Jon, I have not had any replies. I did hear a talk at an American Chemical
Society meeting on a ligand flipping between the two estrogen receptor
subtypes, but it hasn¹t been published from what I can tell. Here¹s a link
to the abstract.
membership.acs.org/C/COMP/pastprograms/Fall06abstracts.pdf
Dear All experts,
I want to check the conformation of one important amino acid in the structure
by looking the difference density map. Should I just omit that amino acid in
the refinement or should I also omit its flanking amino acids? Which one is
better?
Thank you very much for you
Dear Rafael --
I am using PISA to calculate the surface interface of a homdimeric
protein. Does anyone know where I can find the parameters (probe
radius, atomic radii, etc) PISA uses to calculate surface area?
not sure, but would that help?:
http://www.ebi.ac.uk/msd-srv/prot_int/picite.ht
Dear Sun --
I want to check the conformation of one important amino acid in the
structure by looking the difference density map. Should I just omit
that amino acid in the refinement or should I also omit its
flanking amino acids? Which one is better?
The real expert will talk better than
Or Phenix.
Miles
On Feb 18, 2008, at 10:28 PM, Juergen Bosch wrote:
Chavas Leo wrote:
Dear Sun --
I want to check the conformation of one important amino acid in
the structure by looking the difference density map. Should I just
omit that amino acid in the refinement or should I also omi
Chavas Leo wrote:
Dear Sun --
I want to check the conformation of one important amino acid in the
structure by looking the difference density map. Should I just omit
that amino acid in the refinement or should I also omit its flanking
amino acids? Which one is better?
The real expert will
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