Dear all,
I would like to remind you that we are still looking to fill a postdoc
position at AstraZeneca (Cambridge UK) in collaboration with Prof
Ashok Venkitaraman's group at the MRC Cancer Unit. This is an
opportunity for a talented and self-motivated structural biologist to
undertake biophysic
Dear all,
I would like to remind you that we are still looking to fill a postdoc position
at AstraZeneca (Cambridge UK) in collaboration with Prof Ashok Venkitaraman's
group at the MRC Cancer Unit. This is an opportunity for a talented and
self-motivated structural biologist to undertake biophy
Dear all,
there are only a few days before registration closes 28th October for this
year's Protein Structure Determination in Industry meeting. We have a dazzling
lineup of speakers -- please see the full agenda on the website:
https://psdi2019.org/programme/
The meeting will be held at the We
Dear all,
there are still a couple of weeks to register to this year's Protein Structure
Determination in Industry meeting -- registration closes 28th October. We have
a dazzling lineup of speakers this year -- please see the list at the end of
this message or the full agenda on the website:
ht
Dear all,
just a gentle reminder that the early bird registration for the 27th Protein
Structure Determination in Industry (PSDI) meeting, 3-5 November 2019, will be
closing in just a few days' time on the 22nd of July, book now at a
budget-friendly rate!
Exhibitors or sponsors: please use t
discovery), please feel
free to get in touch with the organisers: Judit Debreczeni (judit dot
debreczeni at astrazeneca dot com) or Chris Phillips (chris dot phillips at
astrazeneca dot com). Exhibitors or sponsors: please use the registration pages
to book your place - be quick, only a few premium
Dear all,
I would like to draw your attention to a postdoc position at AstraZeneca
(Cambridge UK) in collaboration with Prof Ashok Venkitaraman's group at the MRC
Cancer Unit. This is an opportunity for a talented and self-motivated
structural biologist to undertake biophysical and cryoEM studi
sessions about biophysics,
crystallography and cryoEM.
If you have an exciting scientific story to share in form of a talk (especially
on HDX and degraders), please feel free to get in touch with the organisers:
Judit Debreczeni (judit dot debreczeni at astrazeneca dot com) or Chris
Phillips
To give a short practical rather than a lengthy philosophical answer:
- in real space: you can try Ramachandran restraints or secondary structure
restraints -- indeed, both can be switched on in Coot in the refinement and
regularisation parameters window (R/RC button in the top right corner). Or
Your solution sounds good. However, another way to skin this cat could be to
define the unnatural residue as an amino acid residue and link it up to the
other amino acid residues using the standard peptide bond description -- which,
I believe, should be picked up automatically if the unconventio
off the top of my head (i.e. not tested):
(add-key-binding "fix atom" "F"
(lambda () (mark-atom-as-fixed (car (active-residue)) (cdr
(active-residue)) 1)))
(add-key-binding "clear fixed atoms" "D"
(lambda () (clear-fixed-atoms-all)))
From: CCP4 bulletin board [mailto:CCP4BB@
Try here for the fashionable Richardson rotamer libraries:
http://kinemage.biochem.duke.edu/databases/rotamer.php
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Dean Derbyshire
Sent: 05 September 2012 09:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] rotomer library
Yes, look here:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example_11:_Paul_Emsley.27s_Key_Bindings
and the key bindings for r, x, t, R.
JED.
>
--
AstraZeneca UK Limited is a company incorporated i
Does your kinase autophosphorylate by any chance? -- That can produce
differently phosphorylated species and affect crystallisability. You can
detect it by e.g. mass spec, and tackle it by dephosphorylating the
protein prior to crystallisation or by coexpression with a phosphatase.
From: CCP
Another vote for python+cctbx.
And a bit of fun:
http://xkcd.com/224/
http://xkcd.com/297/
http://xkcd.com/353/
http://comicjk.com/comic.php/217
http://comicjk.com/comic.php/823
http://comicjk.com/comic.php/842
http://comicjk.com/comic.php/849
From: CCP4 bulletin board [mailto
Hi Krisztian,
I have seen refmac fall over in a similar situation (low-ish res,
partially floppy model) during TLS refinement. You could try to rescue
it by
- using fixed TLS parameters from a previous (successful) refinement
- setting initial B-values to a fixed value
- including the peptide in o
DM is kind of past tense (unless you are dealing with multicrystal averaging)
-- I'd use parrot or shelxe instead (both pretty fast and automated). NCS
operators as input do not seem to be in fashion these days, so you might have
to put up with heavy atoms or partial MR models...
I would not
>
--
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number: 03674842 and a registered office at 2 Kingdom Street,
London, W2 6BD.
Confidentiality Notice: This message is private and may
IIUC, you would like to keep the distance between the ring plane and the Ru
fixed and allow the ring to rotate freely.
I would define bond length restraints between each of the ring atoms and Ru (I
suspect that these distances will be the same for each atom pair) -- the ring
will rotate freel
You can also try
Extensions->Modelling->Replace fragment
(usage self-explanatory)
>
--
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number: 03674842 and a registered office at 2 King
Also, if you happen to use refmac for refinement: it rewrites LINK
records as LINKRs in the output pdb file -- and LINKR records are
unknown to Coot...
JED.
--
AstraZeneca UK Limited is a company incorporated in England an
I've seen flattening of the C1 atom recently in Coot - in that case the reason
was that, as the density wasn't really clear around the sugar, I'd fitted it
180 degrees rotated around the ASN-ND2---C1-NAG bond. In such cases Coot
happily flattens the sugar ring such that C1 C2 C3 C5 O5 are in a p
I think the space-group and cell are missing:
It should be something like:
(transform-map imol rotation-matrix trans point radius space-group cell)
i.e. in your example, say:
(transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962
0.003531
-0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0
Dear all,
I am looking for the sugar-validation tool pdb-care -- the
glycosciences.de website seems to be down, sadly.
Are pdb-care and the other rather valuable glycosciences tools available
somewhere else? I'd prefer to run them locally -- are they available as
stand-alone applications?
Hi,
if you feel you are good at _chem_link sections of dictionary files (and know
how refmac understands them), please read on.
My question in short:
what is the Right Way of defining a covalent link between a ligand that is not
in the standard refmac library and a standard amino acid residue,
Dear all,
I would like to draw your attention to a scientific computing position
currently open at AstraZeneca. This is a fixed term position in the
Computational Chemistry group in Alderley Park to support the high-performance
computing environment as part of the system administration team.
J
Dear all [mmdb users and authors],
I've upgraded to Fedora 9 and now I'm trying to build coot which also
requires mmdb. Now, F9 comes with gcc 4.3 which seems to be
incompatible with mmdb (I think I'm using mmdb-1.0.8) as it gives many
hundreds of the following (and others):
warning: deprecated c
In Coot (0.3.2 and later) you could also try the following:
- center on the serine to be phosphorylated
- click Extensions->Phosphorylate this residue
and Coot will sort out phosphorylation, renumbering etc in no time.
JED
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PR
Unreasonable geometry can be avoided by setting the refinement weight to a
lower value -- either using Extensions->Set Matrix (Refinement Weight) or in
your .coot file:
(set-matrix )
There's also a coot-bb, btw.
JED
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTE
29 matches
Mail list logo
