Just use P1 and "ncs" constraints. What's the problem? Or just keep entire
map and have only symmetry independent copy to work with until finishes,
then make the whole molecule. For real-space refinement it's totally
irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't
clear
I'm sorry but I'm a little confused by your question. If your map
already has four-fold symmetry why can't you simply build your model
once in one quarter of the map? What do you hope to change by
specifying that the space group is P4?
Dale Tronrud
On 5/18/2017 10:06 PM, Qingfeng Chen
Hi,
I have an EM map of a tetrameric protein. It was painful to work with this
map since it is in P1 spacegroup, although 4-fold symmetry was already
applied during map reconstruction.
I noticed that people used MAPMAN to transform spacegroup, however, it
seems not working for me. The map
Dear all,
I want to download PROMOTIF v 2.0 from your ftp server(IP address
128.40.46.11).
However, I can not visit it (ftp://128.40.46.11) because the ftp server was
shut down.
Moreover, I also sent emails to g...@uk.ac.ucl.bioc.bsm or
thorn...@uk.ac.ucl.bioc.bsm. However, both emails
I have looked over a number of high resolution models with NAD+ and
NADH in the PDB as well as small molecule structures. I also have some
familiarity with similar chemistry in the decorations on the edge of
bacteriochlorophyll-a molecules. The CONH2 group does flip over when
the hydrogen
Dear CCP4 Community,
Please see below for details of a 4-year PhD studentship at the University of
Leeds with an industry placement at a pharmaceutical company.
For details on how to apply follow instructions in the link below:
A postdoctoral position is available in Jeyapraksh (JP) Arulanandam’s lab at
the Wellcome Centre for Cell Biology, University of Edinburgh. The JP lab
(http://jeyaprakash.ed.ac.uk) aims to understand the structural level
mechanistic details of processes regulating error-free chromosome
This is excellent news - we have a series of related structures solved in
the YSBL - several sets of which are on different crystallographic origins.
It doesnt matter of course crystallographically but is confusing for
comparison..
Now we can alter them to a common origin with redepositing the
Hi Ed,
The PDB accession code will be based on the primary data stored in the
PDB. Therefore depositors will need to make a new deposition with new
PDB accession code issued if the atomic coordinates are modified using
newly processed intensities from the original diffraction images.
More
Dear Michael,
throwing a few other suggestions into the mix (on top of the good
advice you got already from Graeme and Phil):
* The low resolution I/sigI is quite large and although we have seen
such values for extremely good crystals collected very carefully on
very good instruments, it
It's radiation-damaged. Based on what did you say that it is not?
Also, do you have ice rings or diffuse scattering which might be present in the
higher-res shells in certain rotation ranges but not others, such as from
solvent in the loop?
JPK
From: CCP4 bulletin board
It is puzzling that in the high res shell (to 3.1A) CC(1/2) is 0.533 (OK), but
I/sigI is 0.1 (v low). Is the SDcorrection (SDFAC, SDADD) sensible (and
“Analysis of standard deviations vs. intensity”)? In Aimless the determination
of SDFAC and SDADD sometimes go haywire - with high multiplicity
Hi Michael
What integration program did you use? Different programs can sometimes give
rather different results with very weak data. I'd try everything to see if one
is better than the others.
It's also worth making sure you are up to date. Certainly there are recent
changes in xds and dials
Dear all,
I have a dataset that have two very interesting properties: a) It's in I432,
and b) has a whooping 75% solvent content.
You might think that the solvent content obviously is a big red flag, and so
did I, but I have phased this successfully with just one monomer, and the
packing
Dear Antonio,
we have seen this type of modifications in some of our structures. The
modification of the cysteine (to cysteine-sulfenic, sulfinic or sulfonic acid)
usually arises from exposure to oxygen during crystallization. We managed to
prevent this by either adding TCEP to the protein
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