My "default" MAD strategy is to do single-image inverse beam with round
robin wavelength changes. That is:
energy phi
peak 0
peak 180
remote 0
remote 180
peak1
peak 181
remote1
etc
with one image taken for each line above. I do this until a full
"sphere" is
Great! we can all send our .stl and slic3r files to Artem for rendering!
I want to make individual subunits of a multisubunit protein,
or domains of a protein like Src, and be able to fit them
together to make the complex or multidomain protein.
Topology constraints may require slicing some subun
As an update, this approach did not work in Refmac, but as Pavel
suggested it worked fine with phenix.refine.
--paul
On 08/23/2013 11:51 AM, Tim Gruene wrote:
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Dear Paul,
have you actually tried using the 'alternate location indicator' with
two di
i am not sure this would work as his protein seems to be degraded by the n
end degradation pathway. i feel like it almost needs to be expressed as a
fusion protein with some stabilizing sequence
On Fri, Aug 23, 2013 at 10:08 PM, Roger Rowlett wrote:
> Why not adopt a classical purification strat
Why not adopt a classical purification strategy? IEX-HIC-GEC. His-tag not
required. With your protein strongly basic, anion exchange seems like a
likely first step. After IEX, hydrophobic interaction or salt precipitation
followed by gel exclusion is normally enough for well-expressed proteins.
Ro
Dear Friends,
I have been trying to purify a protein (27 kDa) which has a sumo plus 6 His-tag
at N-ter giving totaly a 45 kDa protein.
This protein does not express without sumo tag and has a poly basic tail (Arg
and Lys) at its N-ter. It does polymerize at acidic pHs.
When I tried to purify it
As a proud owner of the fdm 3d printer I would like to mention that if you
go from vrml to stl and then into slic3r you have to drastically refuce
polygon count or else slic3r chokes trying to process the file.
Cjeets,
Artem
On Aug 23, 2013 5:54 PM, "Edward A. Berry" wrote:
> Thanks, yes, i sho
Thanks, yes, i should have checked out the link on the original post before
asking.
Free programs "blender" or "meshlab" convert vmrl to .stl files which
3d-printers
including makerbot read.
eab
Joel Sussman wrote:
Output should be in *VRML* formal
RasMol, PyMol & Jmol all have options to w
Output should be in VRML formal
RasMol, PyMol & Jmol all have options to write out VRML format files.
Sometimes you need add additional 'struts' to give additional structural
support, Jmol has option of adding these struts.
best regards,
Joel
On 23 Aug 2013, at 21:33, Edward A. Berry
mailto:ber.
Dear all
Could I get some personal reviews on the CrystalHarp plates? Has anyone used it
for actual data collection and structure solution in situ? How does it compare
with X-ray 'transparent' plates?
Thank you.
Theresa
Dear Edward,
Re your em colleagues:-
We are indeed happy to understand their diffraction to 5th order, by which we
mean the d/5 reflection (1st order) because the two are simply different
viewpoints.
Just one loose end:-
The remarkable thing is that the diffraction from a crystal is largely empt
hello everyone
Can anyone point to me where i could obtain the programs twinabs, cell_now
? i cannot seem to locate them by simple googling.
Thanks
mahesh
Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab
Ronnie wrote:
An off-topic question-now that 3D printing is becoming more common, has anyone
tried to print protein structures other
Hi Ronnie,
I have not tried it, but a quick google search for
protein ribbon 3d printer
turns up the following in the results list--
http://ironchefsynbio.wordpress.com/tag/3d-printer/
http://www.lib.ua.edu/sites/default/files/rodgers/Rodgers%203D%20Printing%20Molecular%20X-ray%20Data_V1.pdf
ht
An off-topic question-now that 3D printing is becoming more common, has anyone
tried to print protein structures other than just the surface representation
like in this tutorial?
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/
Is it possible to print a ribbon re
I've had good success transferring crystals grown in
200 mM NaOAc pH 5.5 / 10% PEG
Into a solution for room temperature diffraction (in ~6 steps, peg first, then
buffers) :
100 mM NaOAc / 100 mM Malonate / 30% PEG
And from there into a cryo solution in 4-5 steps) that was:
100 mM NaOAc / 100
increase your PEG3350 >27% and keep the other components at their current
concentration. You can also add glycerol or ethylene glycol into the mix.
If you have multiple crystals then try various variants.
Jürgen
On Aug 23, 2013, at 1:52 PM, Uday Kumar wrote:
Hello
Can anyone suggest a cryopro
Hello
Can anyone suggest a cryoprotectant for the following crystallization condition
0.2-0.4M sodium formate
~20% PEG 3350
0-25 mM Nickel
0-100 mM Malonate
Thank you
with regards
uday
Dear members of CCP4bb
I've used RaptorX to generate a structural model for molecular replacement,
since there isn't any structure on PDB similar enough that i could use instead.
I am trying to find out if this is a common practice within the community and
if people have managed to get molecul
Hi Paul,
I would have them both in PDB file with different non-blanc altLocs and
arbitrary starting occupancies and that will work in refinement (in
phenix.refine for sure, can't tell for other programs).
Pavel
On Fri, Aug 23, 2013 at 8:39 AM, Paul Paukstelis
wrote:
> Greetings,
>
> We have bee
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Dear Paul,
have you actually tried using the 'alternate location indicator' with
two different residues? I would not be surprised if that would work
with refmac.
Best,
Tim
On 08/23/2013 05:39 PM, Paul Paukstelis wrote:
> Greetings,
>
> We have been
Greetings,
We have been working on a few DNA crystals in which the asymmetric unit
contains a stoichiometric (or nearly so) mixture of two similar but
distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but
for a few of these there are some hints from the density for two
diff
I think we are just discussing different ways of saying the same thing now.
But that can be interesting, too. If not, read no farther.
herman.schreu...@sanofi.com wrote:
Dear Edward,
Now I am getting a little confused: If you look at a "higher order" 2n reflection, you will also
get diffracti
Yes, thank you Bob! and therefore, as first pointed out in this thread
by Loes Kroon-Batenburg, and as explainedin (among other places)
the Ladd and Palmer book that Dom Bellini pointed me to,
the indices 001, 010 etc. for example, will index first order diffraction
maxima,
while 002, 020 etc. wi
A point to bear in mind is that only planes with co-prime h k l indices are
"lattice planes" that pass through lattice points. Planes with indices that
are composite numbers nh nk nl are "virtual lattice planes" that do not pass
through lattice points.
Bob
Robert H. Blessing, Ph.D.
Hau
Hi,
Despite the not so large size of the pdf (256 kbs), the file does not want to
get through.
Since a reasonable amount of people seem to have liked a copy for their
students, following some smart suggestions I have put the booklet on Dropbox.
Here's the link: https://www.dropbox.com/s/gljckh
There are only a few places remaining for the wwPDB Workshop on
mmCIF/PDBx for Programmers.
What, why and how?
--
The world of the PDB will be changing rapidly and profoundly over the
next few years. A major change will involve the transition from PDB to
mmCIF/PDBx as the princ
Dear Edward,
Now I am getting a little confused: If you look at a "higher order" 2n
reflection, you will also get diffraction from the intermediate "1n" layers, so
the structure factor you are looking at is in fact the "1n" structure factor. I
think your original post was correct.
To summarize
The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow
to strengthen the biological SAXS environment at the current SAXS beam line at
the MAX-II ring. The position will be for two years and is embedded in the
BIOSTRUCT-X EU program.
Full information of the position is ava
Dear Dom,
No attachment here in either of your messages...
Maybe you can put it up on Dropbox or Google drive and send us the URL?
Thanks,
Petr
On 08/23/2013 04:33 AM, Dom Bellini wrote:
> Hi
>
> Some people emailed me saying that the attachment did not get through.
>
> I hope this will work.
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