Hi Marin,
crystallography has long moved away from the term 'resolution', see e.g.
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2. It is merely a
ballpark number, and it is good to know whether crystallographic data were cut
at 1, 2, or 3 Angstrom, but not very important.
What c
Dear Pavel,
Your paper is one of the more elaborate ones on the issue with an
exhaustive list of references! No wonder, since some 20 years ago, Bruno
Klaholtz was a very successful post-doc in my group at Imperial in London.
However, I have discussed this paper with Bruno at our Brazil School in
2
Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if
it ever made into a peer reviewed journal (couldn't find quickly)?
@Tim Gruene : have a look at d_model in
https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar
lines of what you are hinting here.
Pavel
Hi Tim,
Good to hear from you! No longer at PSI??
See... You are already touching upon one of the logical breaking points in
the resolutiton story...! X-ray crystallography resolution criteria like
R-factors make absolutely no sense outside the field of crystallography and
of structural biology.
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Dear all,
the next MX-proposal application deadline: March 01, 2020 is approaching
https://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html
As usual, all proposals will be handled by our electronic user portal GATE,
https://www.helmholtz-berlin.de/pubbin/hzbgate
Hereby we would li
Dear all,
We are pleased to announce our annual 'Icknield Model Building Workshop' will
take place 16-20 March at RAL/Diamond Light Source, Oxfordshire, UK
This is a comprehensive course for EM model building covering advanced use of
ARP/wARP, Buccaneer, CCP-EM, Coot, FlexEM, ISOLDE, LocScale,
Dear Colleagues,
please make a note of upcoming Phenix workshop focusing on crystallography
and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego,
California. This is a day-long satellite workshop prior to ACA meeting. For
schedule and registration see ACA 2020 web site: www.acame
Dear all,
I am working with a protein that is supposed to bind diacylglycerol
and I would like to know if you know any methods or protocol to handle
DAG during purification and/or for crystallization experiments. Thanks
in advance.
Juanlu
#
Dear Rajnesh,
I wonder about your chosen space group?
I commend that you expand your diffraction data into P1, then run molecular
replacement with Phaser in P1 and if a solution is determined by Phaser run the
coordinates through Zanuda to determine the space group.
Best wishes,
John
Emeritus Pr
Dear Rajnesh,
My experience with molecular replacement is that when you don’t have a model,
you don’t get density. Only in exceptional cases (crystals with a very high
solvent content) I see density for missing loops or domains, so missing density
is very inconvenient, but no reason to be worri
At 3A finding missing domains is tricky.. Can you increase that resolution
at all? Much easier at 2.5A!
But I would refine and rebuild the 4 domains to the best possible maps,
then see if there is any density unaccounted for.
(You will have to lower the COOT default contour level I guess..)
If
Hi,
One other option is to run MR in Phaser in one run with the tetramer made of the 4 monomers as model 1 and the single monomer as model 2. The gui offers this option and there is also an example in the documentaion.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion U
Hi,
you mentioned that there is no electron density for your 5th domain. If
there is nothing coming up even after refinement of the four domains, than
maybe your 5th domain is not there, or so disordered that it doesn't show
up.
Christian
On Wed, Feb 12, 2020 at 9:47 AM RAJNESH KUMARI YADAV
wrot
I am no expert, but a) a very strong peak 7A from the origin means two
molecules 7A apart?? Most unlikely ..
The first thing to look at is the actual images - Lattice translation
defects usually generate very streaky patterns.
Integration programs can cleverly select a lattice and ignore the
unpre
Hi
Something else I should have mentioned - in iMosflm you can sum your images for
viewing only if you have them as HDF5 or Pilatus CBF (as well as summing them
for processing if you have HDF5).
Harry
> On 12 Feb 2020, at 10:18, Schreuder, Herman /DE
> wrote:
>
> Hi Daniele,
>
> I agree
Hi Daniele,
I agree with Wim that the first thing you should check is your space group and
especially whether a ncs symmetry element has been mistakenly identified as
being crystallographic. Since your Patterson peak is along w (c-axis), you have
to change the space group for processing such, t
Hi
Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably
elsewhere) you can sum the images internally to whatever rotation range per
pseudo image you want (so if you have, say, 0.05º physical images you could
process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm 7
Thanks Clemens and Lumbini for your help.
I had tried both the things but none of them worked for this problem.
On Wed, Feb 12, 2020 at 1:56 PM Clemens Vonrhein
wrote:
> Hi,
>
> MOLREP [1] has a nice feature of searching for structures in electron
> density - with the known parts of your model f
Dear Annette,
Which version of iMosflm are you using? Version 7.2.2,
that is currently distributed with the CCP4 suite, will not read Rigaku style
Pilatus images (RIPI) correctly, you need version 7.3.0 that can be downloaded
from the imosflm website:
https://www.mrc-lmb.
Hi,
MOLREP [1] has a nice feature of searching for structures in electron
density - with the known parts of your model fixed. Basically follow
the recipe in [1] (search for "refmac.mtz" - but you can use any other
set of amplitudes/phases as well). In your case the 4-domain model
would be given to
Dear Rajnesh,
Why don't you try refining the 4 domain structure initially. Once the R
factor and R free value is sufficiently low then try to see if there is any
density build up for domain 5.
This has atleast worked for me.
On Wed, 12 Feb 2020, 12:53 Rajnesh Kumari Yadav, wrote:
> Hello everyon
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