Hi Eric
For me it is perfectly normal
Please check Phaser documentation :
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Has_Phaser_Solved_It.3F
All the best
Carlos
On 05/19/2015 02:36 AM, Eric Karg wrote:
Hi all,
Running Phaser using the apo protein as search model on a ~
Hi Manjula,
I had a similar problem: pH, salt, additives and protease inhibitors (I tried
them all) didn't work. The protein degraded after lysis of bacteria within 20
min at 24°C to 50 %. I had luck after i cooled down all buffers and materials
to less than 4 °C or used them icecold ... (1L bo
Hi Eric,
What does your map look like? Do you see features that don't come from the
search model? That's the key. That said, with a TFZ of above 10, I'd be
rather positive about my prospects.
Andreas
On Tue, May 19, 2015 at 2:36 AM, Eric Karg <
052044071b36-dmarc-requ...@jiscmail.ac.uk
Thanks all for the suggestions.
@ Pius,
I used bacterial expression system.Yes I centrifuged precipitated protein
sample and found more amount in soluble form itself, however within a day
protein gets degraded. If I have to further purify the protein I have to
concentrate the IMAC elutes and concen
Open positions in the laboratory of Lari Lehtiö at the Faculty of Biochemistry
and Molecular Medicine and Biocenter Oulu,University of Oulu, Finland.
The research group focuses on structure, function and inhibition of
ADP-ribosyltransferases (ARTDs/PARPs). We use protein X-ray crystallography,
Hi all,
I am purifying a basic protein with pI 7.8. I used 50mM tris 8.8, 300 mm
NaCl, 5% glycerol, 0.1mM PMSFand 5mM beta ME in the buffer and performed
affinity purification. Eluted with 200mM imidazole. While elution I could
see slight turbid in eluted protein (I get pure protein, single ban
Hi all,
Running Phaser using the apo protein as search model on a ~2.5 A dataset of a
protein-DNA complex, I get a single solution but with low RFZ. The map looks
reasonable but I was wondering why the RFZ is so low. Would this solution be
acceptable?
SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66
Also you can treat your SeMET as heavy atom derivative with your native dataset.
J?rgen
..
J?rgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W87
Dear Marcin,
Yes, it worked pretty fine.
As for the "side effect" , I could not, for while, observe any
degradation.
Thank you very much.
Jorge
On 05/18/2015 03:00 PM, Marcin Wojdyr wrote:
That problem has been discussed several times on the coot mailing list.
Currently a workaro
Hi Edward,
I just need to comment on this.
To define contact atoms, you must use "solvated united atoms" that is atoms
with implicit hydrogens where needed (united radius), this radius being further
increased by that of a molecule of water.
Why is that?
In vacuum, it was shown that at a dist
Of course, if you are working with a .docx instead of a .doc file in Word2011
for a Mac, you can always simply insert and “Equation” directly, rather than
the MathType version of Microsoft Equation under the “Insert/Objects” menu.
This seems to work fairly seamlessly, unless you convert the .doc
Thanks Marcin,
I thought I'd patched this already some time ago (shortly after you
mentioned it to me), but now that I try to find it in the logs, it seems
to have been missed/lost.
Paul.
On 18/05/15 19:00, Marcin Wojdyr wrote:
That problem has been discussed several times on the coot maili
sharelatex makes them learn latex, because they can see the output and
the input...
also they can play with lots of examples
2015-05-18 9:57 GMT-05:00 Thomas, Jens :
> Hi Randy,
>
> It's not ideal, but until the bug gets fixed or there's a more elegant
> solution, could you just set up yo
That problem has been discussed several times on the coot mailing list.
Currently a workaround is to type:
(set-use-stroke-characters 1)
in scheme console (Calculate > Scripting > Scheme).
(You can also add it to coot settings).
As a side effect fonts will look worse.
I've just tested a better
Sorry for the spaming... Just want to correct that I plan to say covert the
MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix...
On Mon, May 18, 2015 at 1:44 PM, Chen Zhao wrote:
> I got some answers from the previous thread:
> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk
I got some answers from the previous thread:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html
But I just want to make sure what I am doing...
Thanks a lot,
Chen
On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote:
> Hi Eleanor,
>
> Yeah, the relationship of the XYZ with the unit c
Hi Eleanor,
Yeah, the relationship of the XYZ with the unit cell axes is tricky too.
Although I can get some clues by looking at the position of the
crystallographic symmetry axes on the XY plane, it is better if I could
find a definite answer...
Thank you,
Chen
On Mon, May 18, 2015 at 1:24 PM,
Hi Isa,
don't discard SeMet too rapidly if there are few Mets, modern beamlines,
high-redundancy data collection techniques, and processing and phasing programs
can extract and use small anomalous signal to get structures even if there are
less SeMets than generally accepted by the "rule of thu
Hmm - there are programs which give you the matrix associated with Eulerian
or Polar angles. I think one is pdbset..
Or there is documentation in polarrfn or rotmat which describes how to do
it..
But remember there are conventions about which axes correspond to the
orthogonal X Y Z axes used to d
Hi Weifei -
The first image looks like it was drawn using a vector drawing program like
Adobe Illustrator or Inkscape. If you're looking for something automatically
generated, two of the first hits from a Google search for "protein interaction
diagram" are LigPlot+ (http://pubs.acs.org/doi/abs
Hi all,
I am now trying to convert the NCS axis expressed by theta, phi, chi (or
alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed
into SOLVE. Would anybody suggest me a correct way to do it?
Thank you so much in advance!
Best,
Chen
Hi Randy,
It's not ideal, but until the bug gets fixed or there's a more elegant
solution, could you just set up your own autosave?
It'd mean opening a terminal and running a command before starting, but if you
had a little script like the below running while you were working you'd at
least en
Hi Randy,
I too suggest LaTeXiT. To add to what has already been suggested, LaTeXiT
allows the assembly of a custom library of equations. You can send your
collaborators this library as a file, and they could make minor edits to the
equations in LaTexit gui editor without having to learn the fu
Dear Isa,
Do you have any cysteines? I assume so given you mention class B metals... If
so, and you have a ready supply of relatively isomorphous crystals, I would
consider giving native SAD a go, collecting datasets from 5-10 (or however many
you need) datasets at a reasonably low energy (say
Posted on behalf of Prof. Ren Wei and Jeffrey Reimers.
*Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray
Crystallographic Structures and related work in Biophysics, Biochemistry,
Biomaterials, Chemistry, and Soft Condensed Matter*
Shanghai Universit
> On May 18, 2015, at 4:31 AM, Nicolas Soler wrote:
>
> You just have to learn the (easy) equation syntax
or just use this:
http://www.macupdate.com/app/mac/18172/tex-fog
William G. Scott
http://scottlab.ucsc.edu/~wgscott
The site swift.cmbi.ru.nl/gv/numbers/ is not official, unpublished, and
still poorly maintained. But just for the fun of it, I added a list of
modified cysteines. Be aware that the files are big, so better
download them and read them in the editor than opening them in the browser.
Gert
On 05
Hi Randy, although learning Latex as a whole can for sure be
time-consuming, an alternative solution is to use a Latex equation
editor like Latexit. You just have to learn the (easy) equation syntax
and then you can drag and drop the formatted result into Word or Page,
it's rock solid :
http
Do your collaborators need to edit the equations? If not you can use
LaTeXiT (sorry I'm that person!) which allows you to write your equation
in LaTeX then export directly into word as a pdf. Link below..
http://www.chachatelier.fr/latexit/
Regards,
Jonathan Davies
PhD Student
Department of
There is the possibility of using one of the open-source versions, like
openOffice, but those I guess also have their issues.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read
Sent: Monday, May 18, 2015 4:11 AM
To: CCP4BB@JISCMAIL.AC.
Dear Colleagues,
we are pleased to announce the third CCP4 structure solution school at the
Okinawa Institute of Science and Technology (OIST), Okinawa. All details can be
found at http://www.ccp4.ac.uk/schools/OIST-2015
Title:
"CCP4 school: From data processing to structure refinement and be
Hi All,
We recently obtained a native data set to 2.8A. With no molecular replacement
available we are now moving to heavy atom (not enough methionine coverage for
seleno-met). Unfortunately crystals grow is in 1.4 Na/K H phosphate pH 8 and
we do not have much room for improvement.
Any literat
Hi Randy,
You could try the beta version of the forthcoming version of Word and see if
the bug is fixed. Obviously, it is a beta version and therefore a bit risky
but it installs along side the current version and I’ve been trying it on my
laptop without issue so far. One improvement for me i
Rather off-topic, but maybe someone on the list has found a way to work around
this!
There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one
that is based on a stripped-down version of MathType, which you get with
Insert->Object->Microsoft Equation). You can insert an e
Hi Mohan,
I have seen these too with the C row of morpheus, unfortunately they are most
likely to be salt. Try repeating the same screen but skipping adding extra Mg
to the macromolecule.
Good luck.
Regards
Saba Shahzad | PhD candidate,
Martin Hallberg group
Department of Cell and Molecular Biol
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