ations <https://www.embl.org/groups/kosinski/publications/>.
We offer access to superb computational infrastructure, experimental data from
electron microscopy and other techniques, competitive salaries, and excellent
working conditions.
Best,
Jan
--
Group leader at European Molec
;*
We appreciate your answers
The survey will close on 4 March 2022
*Feel free to contact us at mosbri-d...@ibt.cas.cz *
Jan Dohnálek & Jan Stránský
for the team of
Standards for data archiving & exploitation
MOSBRI
--
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Institute of Biotechnology
Academy of Science
*mydata*.mtz
will only open up the PDB but ont the mtz file. The latter can be opened
via the Load menu.
- The Coot window launched from the phenix gui does not displany the pdb
or the map.
Any pointers would be appreciated.
Thanks!
Jan
--
Jan Abendroth
UCB BioSciences
Seattle
particular interface and
display it.
I hope it works for you,
Jan
On Tue, May 31, 2022 at 8:12 AM Fred Vellieux
wrote:
> Dear bb members,
>
> I am quite certain that someone must have needed to do this already. I
> looked at publications but no details were given concerning how f
of the organisers,
Jan Kosinski
Arjen Jakobi
Maya Topf
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Molprobity is
happy, but when Bong Angels are called in Coot (Regularize zone button
:-)) the bond length goes to 1.36A and Molprobity is unhappy again.
So I would like to ask, who is right or where else the problem can be.
Best regards,
Jan
P.S. CCP4 is version 8.0.002
convinced would be the right ones.
Now, Jan's question triggered mine ..
Anybody else had similar experience with such ligands?
Jan Dohnalek
On Fri, Jul 29, 2022 at 11:54 AM Jan Stransky
wrote:
> Hi all,
>
> while validating X-ray structure using Molprobity (web service), we got
&g
If you know at least something about your protein, organism, type of
molecule, ..., you could try mass spectrometry peptide mapping to known
sequences, this may give you some answers for the ambiguities you might be
seeing, if nothing else ..
Jan
On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper
found here:
https://lbl.referrals.selectminds.com/jobs/xfel-postdoctoral-fellow-crystallography-spectroscopy-4991
https://lbl.referrals.selectminds.com/jobs/chemist-postdoctoral-fellow-4992
Do not hesitate to contact me directly in case of any questions.
Jan Kern
Staff Scientist - Head of
the contacts are nothing great, e.g. position of the oxygens
in the polymer is not clear.
Calculating Polder maps does not clear things up.
How would you deal with interpretation such maps?
Thank you for your ideas :-)
Jan
ting option. Our lab consensus is to keep the atoms, but reduce
occupancy to almost 0. I think, I could do that for the methyl groups in
Jeffamin.
Best regards,
Jan
On 8/19/22 11:42, Matthew Snee wrote:
Hi
It is likely that your density is a consensus of multiple different
jeffamines binding at
.
Jan
On Thu, Sep 8, 2022 at 3:03 AM Tom Peat wrote:
> I think the basic question being asked is why are the B-factors going the
> 'wrong' way?
> That is, as the temperature increases, one might expect higher B-factors
> (at least that is what we are taught) whereas what
, i.e. most of the time used to see "what really happened" during
the last refinement run.
Jan
On Thu, Sep 8, 2022 at 9:29 PM Paul Emsley
wrote:
> A spectre is haunting structural biology - it is the spectre of the PDBx
> format.
>
> We at CCP4 are interested in providing tool
This has been quite variable in (several?) last versions of Coot.
I have some three latest versions available and when one does not work I
start another one. Sad but true.
Jan
On Thu, Sep 15, 2022 at 11:39 AM Robbie Joosten
wrote:
> Not sure if this is a PDBe bug or a Coot bug (o
losing
contrast quite a bit between the really serious issues on ... all the other.
Jan Dohnalek
On Wed, Nov 30, 2016 at 2:33 AM, dusan turk wrote:
> Guys,
>
> I have a two issues to add here:
>
> 1. RSZS validation does not tolerate chain IDs longer than 1 character, so
> i
I had some cases, when path INTEGRATE.HKL -> Aimless gave data, from
which it was not possible to solve structure by Phaser. It looked like
structure solved, but then I got 45-50% Rwork/free. There were no
problems with XDS_ASCCI.HKL -> Aimless (Not scale, just merge) path.
Jan
On 11/2
system is working outside CCP4.)
On "Test server group" GUI ask for login credentials anyway. When giving
htem, I get following:
"""
Testing server_hostname
Failed connection
'NoneType' object has no attribute 'sshThreadRemoteFiles'
"""
Any ideas?
Jan
Good to know, it works indeed.
Just worth noting, that the remote working dir must exist.
Thanks
Jan
On 02/13/2017 02:10 PM, Stuart McNicholas wrote:
Dear Jan,
I see the same error message when doing "Test server group".
However, when I actually run a job, all seems OK. I thin
t the data
are there in temp directory.
Any ideas? Developers, any idea how to help you track down the bug? Is
it possible to import resulting data back, including database entry?
Jan
On 02/13/2017 03:21 PM, Jan Stransky wrote:
Good to know, it works indeed.
Just worth noting, that the remote w
geometry is difficult to achieve in most standard
MX beam lines. I thought there was some initiative maybe 8-10 years ago at
APS and at ESRF to get a He cryo jet running at one of their MX beam lines
but I do not remember the details.
Greetings,
Jan
On Tue, Apr 4, 2017 at 2:14 AM, Colin Nave wrote
We had experience with a relatively small glycoprotein - when glycosylation
sites were deleted, solubility went drastically down - we could not express
soluble any more. Back to eukaryotic expression system which worked.
So may be you were really lucky.
Jan
On Tue, Apr 11, 2017 at 10:34 PM
Dear ccp4ers,
is there way to retain HETATM keyword for ligands when running refmac?
It apparently changes HETATM to ATOM which spoils some nice ligand
features in Coot...
Best regards,
Jan
Indeed, even from i2. The issue is somewhere else, sorry for blaming refmac.
Jan
On 05/03/2017 01:09 PM, Robbie Joosten wrote:
Hi Jan,
That could be a postprocessing thing, because that version of Refmac works fine
from the command line or from CCP4i (at least in my hands on Linux).
Cheers
Hi Jan, Hi Rob, hi Gustavo,
thanks for you answers. I totally missed the thread in the bb and
couldn't find anything in the archive also the wiki entry - frankly
I havn't checked that one for a while ...
Great to know that the CU update solves most of the issues regarding t
Best regards,
Jan
So, thanks to pointing by Paul, I have found the keybinding definition
in "python/template_key_bindings.py" on coot's github. It is called
"Step scrollable map number" with suggested key "M"
Jan
On 07/12/2017 10:33 AM, Jan Stransky wrote:
Hi,
I believe,
/jan-florian-kern/) at Berkeley Lab’s
Molecular Biophysics & Integrated Bioimaging Division. We have been
conducting a number of XFEL experiments on several different systems and
some recent publications include:
Fuller et al, Nature Methods 2017
http://www.nature.com/nmeth/journal/v14/n4/abs/n
http://biosciences.lbl.gov/profiles/jan-florian-kern/) at Berkeley Lab’s
Molecular Biophysics & Integrated Bioimaging Division. We have been conducting
a number of XFEL experiments on several different systems and some recent
publications include:
Fuller et al, Nature Methods 2017
com>
Jan Abendroth, Beryllium Discovery,
jabendr...@be4.com<mailto:jabendr...@be4.com>
Thanks and best wishes,
Matt Clifton
Jan Abendroth
JAN ABENDROTH, Dr.
Core Leader, CrystalCore
P 206-780-8925 F 206-780-8547
Seattle | Boston | USA | be4.com
[cid:image001.png@01D350FE.EE91E390]
You could try Xenon derivation chamber.
DOI: 10.1107/S0907444902011010
Cheers,
Jan
On 29/11/17 13:05, Eleanor Dodson wrote:
> That depends on the quality of your data and your model!
>
> I play with refinement and rebuilding - check indicators v
> resolution., etc etc (I look at the
://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/
or the attached file for details.
*Apply before February 9 2018 to frederic.velli...@ibt.cas.cz
.*
Jan Dohnalek
Institute of Biotechnology, Biocev
Centre of Molecular Structure
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy
*Postdoctoral positions available in cryo-EM methods development at the
MRC Laboratory of Molecular Biology, Cambridge UK, in the groups of
Chris Russo and Jan Löwe*
We have one position each available, funded for two years as part of the
LMB’s Blue Sky collaboration with AstraZeneca. The
h and easy.
Jan
On Wed, Mar 15, 2023 at 3:52 PM Randy John Read wrote:
> Hi Jon,
>
> My understanding of the philosophy is that new users would prefer to think
> about crystallographic data objects, rather than worrying about the arcana
> of MTZ files and the many different flavo
So sad.
Alexei was a great scientist and a good friend.
I will have only good memories of him.
Jan
On Mon, Mar 27, 2023 at 5:20 AM Nukri Sanishvili wrote:
> Sad news indeed for so many of us, those who knew Alexei personally and
> those who benefited professionally from his se
We are getting the same feeling from discussions with (non-structural)
biologists around us.
I also agree that AlphaFold models are a great tool but they do not tell
everything and cannot exactly replace experiments.
Is the development mainly in the hands of journals' reviewers...?
Best
constriction
through focussed ion beam (FIB) milling and electron cryotomography
(cryo-ET) of Gram-positive bacteria.
The new 3-year position will be located at the MRC Laboratory of
Molecular Biology (LMB) in Cambridge, UK within the group of Jan Löwe,
working in collaboration with the groups of Séamus
to us ...
Avoid FedEX!!!
Jan Dohnalek
On Fri, Jul 28, 2023 at 5:16 AM Dr. Kevin M Jude wrote:
> My first adventure in international crystallography is off to an
> inauspicious start. On Monday, I sent a dry shipper “overnight” from
> California to Saskatchewan, but it has been stu
for a good week. With simple
tests one can identify dewars that are on their way out.
Glad that your dewar turned up and that the great staff at CLS could fit
you in.
Cheers,
Jan
On Fri, Jul 28, 2023 at 1:09 PM Dr. Kevin M Jude wrote:
> Hi all, thanks for the responses on and off l
If I delete my .CCP4* and CCP4I2_* directory to start fresh, the GUI
fails immediately. Probably because it tries to open a view, which
triggers the same error as above?
Any help is highly appreciated...
Best
Jan
--
Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann
Institut für Bi
didn't really fit my error, but currently everything is
running (again).
Sorry for the spam...
Best,
Jan
--
Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann
Institut für Biochemie | University of Cologne
Zuelpicher Str. 47 | 50674 Cologne | Germany
📞 +49 (221) 470 3212
.
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
To unsubscribe from the CCP4BB list, click the
Structure under MOSBRI umbrella: CD, ITC, DSC, MST (labeled,
non-labeled), BLI, nanoDSF, DLS, mass photometry, SPR, SAXS,
FT-IR, fluorimetry, UV-Vis, optical tweezers
See you at the instruments!
Best regards,
Jan Stransky,
on behalf of CMS, MoB-IBT team
We have seen quite a few of these.
Oxidation of S.
Mostly in our case a result if reaction with beta-mercaptoethanol..
Jan
On Mon, Dec 18, 2023 at 6:14 PM Liliana Margent <
lmarg...@gradcenter.cuny.edu> wrote:
> Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc
, etc., who want to learn a technique enabling high
throughput screening for dynamic parameters of biochemical interactions on
a single molecule level.
The deadline for submission of an application to participate in this course
is: Thursday 29th February 2024.
Jan Dohnalek
MoB-IBT centre of MOSBRI
course
is: Thursday 29th February 2024.
Jan Dohnalek
MoB-IBT centre of MOSBRI
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
/
<https://www.mosbri.eu/training/basic-level-schools/bls2/>*
or contact directly the course organizers for more information
zdenek.lan...@ibt.cas.cz (Scientific Organizer)
magdalena.schneider...@ibt.cas.cz (Course Admin)
Jan Dohnalek
MoB-IBT centre of MOSBRI
--
Jan Dohnalek, Ph.D
Instit
-linking mass
spectrometry, competitive salaries, and excellent working conditions.
Best,
Jan Kosinski
--
Group leader at European Molecular Biology Laboratory (EMBL) Hamburg
Joint appointment Structural and Computational Biology Unit EMBL Heidelberg
Group leader at Centre for Structural Systems
Jan Dohnálek
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758
To unsubscribe from the CCP4BB
register here
https://cssb.structbio.org/ccp4-em-training-workshop-page/
*Registration deadline 3 February 2025*
Looking forward to see you in Nové Hrady
Jan Dohnálek
on behalf of the organization team
The Course is financially supported by the Czech Society for Structural
Biology, CCP4/CCPEM
tee.
...
-
The Max Perutz Prize awardee announcement is expected in June/July of this
year. The candidate receives the award at the official opening of the
following ECM in Poznan and presents a lecture at this occasion.
une or July of this year. The
candidate receives the award at the following ECM in Poznan and presents a
lecture at this occasion.
Jan Dohnálek
Vice-president of ECA
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Veste
munity.
...
-
The awardee announcement is expected in June or July of this year. The
candidate receives the award at the following ECM in Poznan and presents a
lecture at this occasion.
Jan Dohnálek
Vice-president of ECA
-
tee.
...
-
The Max Perutz Prize awardee announcement is expected in June/July of this
year. The candidate receives the award at the official opening of the
following ECM in Poznan and presents a lecture at this occasion.
une or July of this year. The
candidate receives the award at the following ECM in Poznan and presents a
lecture at this occasion.
Jan Dohnálek
Vice-president of ECA
--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Veste
://ecanews.org/erwin-felix
-lewy-bertaut-prize/)
*Please spread this announcement in your local crystallographic community.*
The prize award ceremony will be at the International Conference on Neutron
Scattering 2025 in Copenhagen-Lund, July 6-10, 2025,https://icns2025.dk/.
Jan Dohnálek
Vice
Hi everyone,
I'm running into issues installing coot on Macosx Catalina. When install the
system using BINARY.setup the following message shows up:
Does anyone else faced this problem? Is there a way to work around it?
Thanks,
J.
##
Dear all,
We’re looking for a 24 h.t. and 24 fil. power supply for a Phillips CM10
Electron Microscope. Does anyone know how to get such component separately?
Used is fine too.
Thanks,
J.
To unsubscribe from the CCP4BB list
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan
suggestions in this regard will be very helpful and highly appreciated.
Thanking you,
Jan
*Dear All,
Could any body share experience of soaking with **
Pentamethylcyclopentadienyl-**iridium-chloride dimer? I am planning to soak
my crystals with this compound and some details for e.g soaking time and
minimum concentration will be helpful.
Thanks a lot,
Jan
*
Dear all,
I recently obtained some spherulites while trying to crystallize my protein.
The spherulites are manually reproducible, but changing pH, protein
concentration, and salt concentration does not result in crystal formation.
Microseeding with crushed spherulites isn't a solution either as it
Thanks for the protocole and advice! I'll put my spherulites on gel. It will
make things clear.
Jan
2011/8/24 Regina Kettering
> Something to consider is the quality of the PEG 3350. We have found that
> different qualities of PEG 3350 can give different results, depending on the
(using MRC crystallisation plates, of course).
For more details:
http://www2.mrc-lmb.cam.ac.uk/groups/JYL/WWWrobots/robot.html
best,
jan
worked. This was for the purpose of doing liquid state NMR on that
protein.
I does help to solubilize the two aa in 1:1 ratio as the two combined
improve their individual solubility.
Jan Jensen
On Thu, February 28, 2008 4:33 pm, Paul Paukstelis wrote:
> posting for a colleague:
>
> In Golova
Hi everyone,
I'm working on structure of an antibody that inhibits a receptor. The
antibody doesn't induce any conformational change in the receptor and
doesn't bind the ligand binding site. If we superimpose the receptor
with antibody and ligand the only hindrance we find is a electrostatic
repuls
a dramatic effect on ligand binding. So I
was thinking about a double effect: repulsion + loss of one salt
bridge.
Best,
Jan
2013/10/8, herman.schreu...@sanofi.com :
> Dear Jan,
> since electrostatics go with one over distance-square, there may still be
> some electrostatic repulsion i
that the
asp is too close to the antibody arginine.
Our binding essays were done by fluorescent labeling of the ligand.
Clustering shouldn't play a role. It's hard to explain, there is no
steric hindrance. I guess I'll have to drop this idea of repulsion.
2013/10/8, Andrey
the antibody stabilizes the ligand receptor interaction. What we see is the
opposite.
Do you have any references about asp-arg as "hot spots"?
Thanks,
Sent from my iPod
On Oct 8, 2013, at 12:58 PM, "Nadir T. Mrabet"
wrote:
> Jan,
>
> Ionic interaction d
I apologize for being a bit naive, but it turns out that I'm working
an low resolution mode (3.6 A). A great part of the chains have
previously been built with polyalanine, since there's obviously no
density for the side chains. When using phenix, I obtain a model just
as good with all residues mut
Dear all,
I'm filling out my table for NSMB, about a structure of protein ligand
bound to a receptor. They ask for 3 different lines regarding number
of atoms & bfactor. 1) Protein 2) Ligand/Ion 3) Water.
Does my protein ligand belong to Protein or Ligand/Ion?
Thanks,
Thanks for all responses,
Yes I'll keep my ligand in the protein section, and will add extra
information regarding the ligand/receptor. They actually asked for
separate b-factors during review, so I guess they'll be willing to see
it in the final table.
Jan
2014-02-18 11:39
Dear all,
I'm refining a structure with three modified amino, ccp4 code: CY3, DTR,
and MPT respectively. However I don't know how to give phenix.refine the
adequate libraries as to obtain the correct geometry for three amino acids.
I tried to add the cif libraries downloaded from ccp4 to the comman
Hi everyone,
I’m trying to publish two structures at 3.1Å resolution with the following
refinement statistics:
Resolution range (Å) 49.2-3.1
49.3-3.1
Rfactor (%)24.0 (32.4)
ments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu <mailto:diana.tomch...@utsouthwestern.edu>
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
Hi everyone,
Looks like the undo button on Coot doesn't work. I installed Coot-0.8.6 on
MacOsx El Capitan. Anyone knows what could be the problem? Or where to
report the bug?
Thanks,
), and
is there some method to reintegrate iron sulfur cluster back into the
protein molecule under these conditions. Can anybody suggest some
literature, protocol or something that can improve the protein aggregation?
I look forward to hearing from you.
Best wishes,
Jan
suggestions and
discussions on this issue.
Thanks very much!
Jan
yielded any
good results. I have read about mapping interaction through non-natural
amino acids.
Has someone done it in recent times. Is it possible to suggest some
literature, resources or protocol that can be useful. I will be highly
grateful.
Thanking you all.
jan
Hi everyone,
I recently switched from HKL2000 to imosflm to get rid of ice rings.
The group space and cell unit of the data set are known and perfectly
recognized by HKL2000. The predictions are also correct.
In imosflm, the unit cell and space group are recognized. However the
predictions are ter
Dear All ,
Could anybody suggest the best possible manner to measure the halflife time
of a protein-ATP complex? Our protein binds to ATP and we would like to
measure its half life time after it is bound to radiolabelled ATP. Looking
forward for your valuable suggestions.
Best wishes,
Jan
?
Thanks,
Jan
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ho
Hi Everyone,
Does anyone know what’s the fastest way the find all commercially available
proline derivatives on carbon gamma?
Thanks,
Jan
Thanks everyone for all the suggestion! I have plenty of options now!
> On Mar 31, 2017, at 11:06 AM, Lakshmi SwarnaMukhi Pidugu
> wrote:
>
> You could try scifinder.
>
> Swarna
>
> On Wed, Mar 29, 2017 at 6:07 PM, Jan van Agthoven <mailto:janc...@gmail.com>
Sorry for being a bit off-topic, but I’m looking to transform the catalytic
properties of a protein I’m working on by adding an aromatic moiety on one of
its prolines. However none of the proline derivatives I find commercially are
really interesting. Does anyone know what would be the cheapest
-Jan Waterreus
Thanks your suggestions! I tried Dials but couldn’t get any further. There just
too few spots like Artem suggested. I’ll follow Patrick’s advice to seed a new
screening with this crystal. This one was really tiny. I may get a bigger one.
Jan
> On Feb 17, 2018, at 2:43 PM, Harry Powell wr
Dear all,
We’re working on an unknown ligand density in our CryoEM structure. Is there a
program that uses deep-learning to fill uncharacterized electron density
similar to Checkmyblob but for CryoEM maps?
Thanks,
Jan
Thanks Pavel! I tried, choosing Fobs and sigmaF as input variables, but sadly
it returned an error message (see below). I don’t know if anything can be done
to adapt the mtz file to their server. So I emailed them and will share if I
get some feedback.
> On Jan 26, 2024, at 2:45 PM, Pa
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