No - it is not.
I have seen similar problems.
Your atom records arent labelled as HETATM are they?
That triggers strange behavior.
Eleanor
On 7 November 2017 at 07:13, Abhishek Anan
wrote:
> Are you adding the cif file of the unnatural amino acid on LIB in path
> in refmac.
>
> Best,
> Abhish
Are you adding the cif file of the unnatural amino acid on LIB in path
in refmac.
Best,
Abhishek
On 11/7/17, Rashi Aggarwal wrote:
> Dear all,
>
> I have an unnatural amino acid in my structure which I could successfully
> add in coot. The amino acid is taking the right bonds when viewed with
Dear all,
I have an unnatural amino acid in my structure which I could successfully
add in coot. The amino acid is taking the right bonds when viewed with
coot. However, the pdb file has a ter line just above the residue.
If I remove this line and submit the pdb to refmac it again adds the ter
li
See Table 1 and corresponding discussion here:
http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf
Hope that hints you the answer. If not get back to me with questions.
All the best,
Pavel
On Mon, Nov 6, 2017 at 7:18 PM, Eze Chivi wrote:
> Hi, my PDB file lists only 4 resolution b
Hi, my PDB file lists only 4 resolution bins (full range: 1.6-19.1A). This is
the first time I noted this behavior (It's used to be 20 bins). It is OK for
deposition? It is need to rearrange statistics? How I can do that? Thank you
very much. (I did my refinements in phenix, oops!, but the ccp4b
Hi,
I have looked in the archive for posts about this, but there hasn't been
one for about a year. Can anyone comment on whether they have managed to
get a linux flavor and GeForce cards to work with pymol and/or coot 3D
stereo? Geforce cards supposedly support openGL, but posts from October
last
Dear all,
We would like to draw your attention to the first EMBO workshop on "Molecular
Neurobiology", taking place on the beautiful island of Crete on 8-12 May 2018.
http://meetings.embo.org/event/18-neurobiology
The meeting brings together structural biologists & biophysicists with
researche
Dear Colleagues,
I am pleased to invite you to attend the 5th BioXFEL International Conference.
Please feel free to distribute the information below to interested parties.
Please refer to our website to see the most updated speaker list I apologize in
advance for any duplicates. We hope to s
Dear all,
in our institute we thought about buying the Microfluidizer LM-20 for
cell disruption
(https://www.microfluidicscorp.com/microfluidizers/lab-machines/lm20/).
It would be nice if you shared your knowledge with us concerning the
handling, robustness, the frequency of repairs or spare
One unintended consequence of an increasingly translational research focused
agenda is
that science is steadily drifting towards milestone-oriented contract
research. We are almost there
already, with practically every grant gendered and mile-stoned with
trumped-up relevance to the greater
goo
Hello,
I want to use carba-NAD+ (carbanicotinamide adenine dinucleotide), a
non-hydrolyzable analogue of NAD+ for structural and functional studies of
an enzyme. I have seen this compound used in several publications, but the
publications either did not disclose the source of the compound or it w
Dear Martin,
A more bleeding-edge type of experiment in the vein David is
indicating would be to use a "rotation SFX" protocol to record
complete data off one or very few crystals that will be completely
exempt from radiation damage, as described in doi:10.1038/nmeth.2962
and in doi: 10.1073/
Dear Martin,
For well-refined structures with low residuals, +/- 3 sigma levels (the
standard coot contour levels) are very small on an absolute scale. How does
your 2Fo-Fc map look like? Are there really big holes in the FAD for the
missing atoms with almost zero 2Fo-Fc density?
As others hav
Hello,
ENDscript should do the job: http://endscript.ibcp.fr
All the best,
XR.
On 06/11/2017 11:18, Abdul Ajees wrote:
Dear All
We would like to analyze a protein molecule, which has two
chains. Both the chains are
Some alternative interpretations have been suggested, but if you think
you are seeing radiation damage, you could try collecting data on
several crystals and binning it by dose received. For comparison see:
The catalytic pathway of horseradish peroxidase at high resolution.
Berglund, et al. (2
Hi Martin,
I am not sure which class of flavoprotein you are working with, but in many
cases, one can alter the redox state of the FAD (or FMN) in the crystalline
lattice and this sometimes changes the conformation of the isoalloxazine ring
of the flavin and deviates from a simple planar isoall
The group of Prof. Dmitry Veprintsev at the Centre of Membrane Proteins and
Receptors, University of Nottingham is looking for PhD and postdoc
candidates.
The overall research direction of the lab is developing approaches for
incorporation of protein and systems dynamics of G protein-coupled
recep
Dear Martin,
we experienced the butterfly-like structure of FAD in monoamine oxidases
but this was observed also in other flavoenzymes. Whether this is an
intrinsic feature of these enzymes or something due to radation damage is
not clear for each case. However, in our experience this bent conform
Dear Martin,
a couple of years ago we had a similar problem with FAD degradation. In
our case it was not caused by radiation damage, but we saw different
ratios of intact and degraded FAD depending on the age of the crystals
[Winkler et al., Nat. Chem. Biol. 4, 739-741 (2008)].
Best regards,
Dear colleagues,
I am investigating a structure of a FAD-dependent enzyme. The electron density
map suggests radiation damage to the FAD. It apparently is different from
simple change of the redox state and "butterfly"-like structure. We did not
find in literature possible products of radiation
Dear AllWe would like to analyze a protein molecule, which has two chains. Both
the chains are structurally identical and have high sequence similarity. But
both the chains have tendency to form different binding pockets with different
ligands. In PDB, the chain A has five structures crystallize
Dear all,
one of the most interesting documents in recent times on the matter of
translational research and IP comes from the Wellcome Trust:
https://wellcome.ac.uk/sites/default/files/transforming-uk-translation-20170725.pdf
In particular, under committments 4-8, they spell out - although impl
Dear all
I have a position in my team which would be well suited for someone with a
structural biology/bioinformatics background and some programming experience
looking to move away from research and into a professional software development
career path. The work involves maintaining, improving
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