Dear Colleagues,
We currently have several positions available in my group at the
University of Warsaw - both postdoc and PhD. The research project
combines quantum crystallography with protein crystallography, focusing
on 3DED/microED techniques.
We're interested in hearing from researchers
Dear all,
The deadline to submit papers for Microscopy & Microanalysis (M&M2025) that
will be held in Salt Lake City, Utah on July 27-31, 2025 has been extended.
The final, extended submission deadline is Tuesday, February 18, 11:59 PM, U.S.
Pacific Time. Afterwards, no exceptions and no furthe
Dear all,
The deadline for applications for the FEBS workshop ‘Time-resolved
spectroscopy meets time-resolved crystallography. The future of dynamic
photobiology.’ (https://dynamicphotobiology2025.febsevents.org) is
postponed to February 10. The workshop will take place from May 6-8 2025
in t
Dear Colleagues,
The registration and abstract submission deadlines for the upcoming West Coast
Structural Biology Workshop have been extended!
The UPDATED deadlines for registration and abstract submission are Feb. 28,
2025 and Feb. 21, 2025 respectively.
The meeting is scheduled for March 23
Thanks to everyone for the quick replies! I’ll start by fitting PEG and let
you know how it goes.
Best wishes,
Chris
On Mon, 3 Feb 2025 at 18:22 Boaz Shaanan wrote:
> So it does to me too. There are a few PEG variants in the monomer library,
> have you tried them? Most PEGs, if not all, are mi
Dear Colleagues,
We are delighted to announce the *Scientific Programme *for the *7th
International Symposium on Diffraction Structural Biology (ISDSB2025)*,
taking place from *5–7 May 2025* at the *European Photon and Neutron
Science (EPN) Campus in Grenoble, France,* at the European Photon
So it does to me too. There are a few PEG variants in the monomer library, have
you tried them? Most PEGs, if not all, are mixtures in terms of chain length.
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On Feb 3, 2025 19:12, Dale Tronrud wrote:
Looks l
Looks like a pretty good PEG fragment to me.
Dale Tronrud
On 2/3/2025 8:42 AM, Chris Fage wrote:
Dear All,
Our ~2.3 Å crystal structure contains a tube of electron density for an
unknown ligand, into which we've built a network of water molecules (see
attached images with 2Fo-Fc map conto
Hi Eleanor,
Thinking about this you are most likely correct that COOT has created this
issue. The coordinates were in PDB format.
Best wishes,
Joanna
From: Eleanor Dodson
Sent: 03 February 2025 15:17
To: Joanna Zukowska
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [
I think it is probably a COOT issue - if you add a TERMINAL RESIDUE in COOT
after res 430 say, it should delete the previous TER record..
A TER record is meant to flag the end of a protein chain, so I guess really
REFMAC is to be congratulated for acknowledging that, and the other
programs congratu
Unfortunately we cannot share this file due to an NDA. However we think the
problems were due to some missing residues being built in through the "get
monomer" option which COOT and molecular replacement (PHASER) does not seem to
have a problem with, but for some reason REFMAC does. Molecular re
Hi all,
Just as an aside, I have had this happen in the past using both Refmac and
Pheinix.refine. Just happened last week when I was adding a residue to the end
of chain. If the TER card is not present then and residues after it with the
same chain ID are treated as ligands.
Len
Leonard M
Could you send the rogue coordinate file or is it confidential? it might
perhaps be valuable to find WHY it caused such problems..
On Mon, 3 Feb 2025 at 14:22, Joanna Zukowska <
000100b050ebf83d-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi all,
>
> Thank you for all your advice. We ended up re-runn
Hi all,
Thank you for all your advice. We ended up re-running the coordinate file
through molecular replacement and it seems to have corrected all the problems
within the file mentioned.
All the best,
Joanna
From: CCP4 bulletin board on behalf of Keitaro
Yamas
Thanks for telling me that..
E
On Mon, 3 Feb 2025 at 12:55, Keitaro Yamashita <
keitaro-yamash...@g.ecc.u-tokyo.ac.jp> wrote:
> Dear Eleanor,
>
> > From log: refmac thinks there are 433 (A) or 426 (B) residues
> > but the VDW restraints seem to involve higher number residues . (of
> course you m
Dear Eleanor,
> From log: refmac thinks there are 433 (A) or 426 (B) residues
> but the VDW restraints seem to involve higher number residues . (of course
> you may not have numbered things from 1...)
> But why does it think the ligands include peptides??
This is because gemmi (which generates
Hmmm = Keitaro is right - there is something odd for the last few residues..
I would look carefully at the input coordinates about 430
>From log: refmac thinks there are 433 (A) or 426 (B) residues
but the VDW restraints seem to involve higher number residues . (of course
you may not have numbere
Dear Joanna,
There might be an unnecessary TER card in your PDB file between
residues 430 and 431 of chain A. Could you check that? The log file
suggests that residues after 430 are being recognised as a non-polymer
part.
Best regards,
Keitaro
On Mon, 3 Feb 2025 at 20:12, Joanna Zukowska
<000100
-- Forwarded message -
From: Lutz, M.H. (Martin)
Date: Mon, 3 Feb 2025 at 08:59
Subject: ECA Crystallographic Computing
To: Lutz, M.H. (Martin)
Dear colleagues,
this e-mail contains information about the activities of the special
interest group SIG-9 (Crystallographic Computing
That is VERY odd - can you send a log file?
And are you sure you arent accidentally requesting "unrestrained
refinement"?
In REFMAC that would be triggered by a keyword
REFI UNRE
Eleanor
On Mon, 3 Feb 2025 at 09:37, Joanna Zukowska <
000100b050ebf83d-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi al
Hi all,
Currently my colleague and I are experiencing a problem with peptide bonds
breaking after refinement. Has anyone else experienced this or knows how to fix
this problem? Selecting detect and apply covalent linkages in the restraints
does not help.
Best wishes,
Joanna
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