Structure-Function Studies of Protein Trafficking
The Role: A PhD scholarship is available immediately in the lab of
Dr. Brett Collins at the Institute for Molecular Bioscience,
University of Queensland, Brisbane (Australia). The successful
applicant will join a team using multidisciplin
Dick Dickerson tried to do the same thing at Caltech around the same time.
The major problem with cooling equipment was that the Picker goniometer
had lots of metal in it, and each of the metal pieces cooled and
contracted differently, so the alignment was always off. Nice idea, but
not useful. Tha
Roberto,
An also less than optimal work around might be to take your refined
.pdb from PHENIX or CCP4 and run it through the downgrade utility on
MolProbity to change to PDBv2.3 format before working in Coot. I
don't think it is necessary to convert back to PDBv3.0 for
phenix.refine, but MolProbi
I've been in that cold room / hutch. I never heard of it being flushed
with LN2. I think that is just to make the room sound cooler.
Jim
On Thu, 19 Jun 2008, Mischa Machius wrote:
Sadly, I have never seen the room being used. Perhaps one of the 'older'
Martinsrieder on the forum has seen it
Sadly, I have never seen the room being used. Perhaps one of the
'older' Martinsrieder on the forum has seen it. MM
On Jun 19, 2008, at 12:11 PM, Klaus Futterer wrote:
"... room that was lined with insulated steel walls and that could
be flushed with liquid nitrogen."
I'm trying to pictur
"... room that was lined with insulated steel walls and that could be
flushed with liquid nitrogen."
I'm trying to picture this ... did you guys have some kind of LN2-
proof SCUBA diving equipment to work in there?
Klaus
---
Ha, everyone seems to be bragging about how far back cryo-
crystallography really goes. In that vain, I'd like to mention that,
in Martinsried, we had a room that was lined with insulated steel
walls and that could be flushed with liquid nitrogen. It was requested
(demanded, really...) by Ro
I think that we will have to 'remediate' Coot (and the whole of
CCP4 for good measure). I advise all SHELXL users NEVER to deposit
hydrogen atoms, it saves lots of hassle.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettinge
Well everyone, talking of early applications of cryocooling to X-ray
crystallography, what about Sten Samson's marvellous helium cryostat
which was operational at Caltech since the end of the 1970s and used to
reach temperatures around 20 K routinely , see for example:
Proc Natl Acad Sci U S A
Any idea is appreciated how to add Hs (hydrogens) stereochemically to protein
or peptide without altering the coordinates of non-hydrogen atoms. Does COOT
have any option to do this ?
Thanks. Sam.
__
Hi Paul,
How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT
without altering the coordinates of non-hydrogen atoms.
Thanks. Sam.
> Date: Thu, 19 Jun 2008 15:57:46 +0100
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] Coot and
It's due to PDB versions 2.3 and 3.0. It's a pain, and Paul is aware of
it. The solution you describe works and it's always nice to check with
Molprobity. I've tried using the PDB tools to change 3.0 to 2.3 but they
also have problems :-(
For us poor souls who are suffering with hydrogen a
Dear Roberto,
Roberto Steiner wrote:
Dear all,
a problem possibly at the coot/mmdb interface...
Indeed.
If one uploads a pdb file (from phenix.refine in the example below)
that contains Hs into Coot and then writes it out (with or without any
modification done on it) Coot shifts the HG2n
I typically collect data at -50C on all small molecule samples. I've had
quite a few cases where there are phase transitions, and you can damage
the crystals, especially when the molecules are packed in a pi-pi stacking
motif, or I'm dealing with alloy systems.
I've also collected data at 16K, so
Every small molecule dataset I collected as a graduate student in
chemistry back in the mid to late 1980's was at 100K. I never had to
worry about crystal slippage during collection, organic solvent
evaporation, air oxidation of the sample (organometallic metal
clusters) or secondary radiat
Dear all,
a problem possibly at the coot/mmdb interface...
If one uploads a pdb file (from phenix.refine in the example below)
that contains Hs into Coot and then writes it out (with or without
any modification done on it) Coot shifts the HG2n of THR on the
right by one column space. Beca
I would go along with Harry & friends, I used crystal cooling when I was
at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the
technique had already been in routine use there for at least 10 years,
in order to study compounds that are liquid at ambient temp (of course
it was custom-built
I am currently refining a high-resolution structure that has many reflections
(~180,000). I
would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so.
Any advice
will be greatly appreciated.
there is a bunch of commands in dataman to do this (and other things) to your
tes
This fellow below is presumably and Indian,
writing in English at a German University,
a very confused new generation researcher, indeed.
Maybe this will help:
S.Jayashankar
(Ein wenig verwirrter Forscher der neuen Generation)
Forschungsstudent
Institut fuer Biophysikalische Chemie
Medizinische Sc
Hi
Without wishing to start an argument, I've been checking with some of
my colleagues who are chemical crystallographers - the reply I get is
that, for routine structural analysis, "pretty well all datasets are
collected at 100K unless the crystals fall apart at low T, or if the
cryostre
Typically crystals of small organic compounds do not require freezing as
there are no solvent channels. They do in general not suffer from
radiation damage at room temperature the way protein crystals do.
Occasionally they are mounted in a capillary instead of simply glueing
them to a goniomete
Hi
I just noticed I scrambled that first paragraph. I didn't intend to
imply you should be able to see your referees (or their criteria) at
least some of the time. It should have read something more like-
yes, both of those. Plus "freezing out" multiple conformations so
that you can mode
Hi Colin
yes, both of those. Plus "freezing out" multiple conformations so you
can model them properly - bear in mind that a small molecule
structure at a resolution worse than 1Å would be challenging to get
past the normal criteria of referees, so you should be able to see
them at least
Harry
Can you clarify why you get "a substantially better structure at cryo
temperatures"
e.g higher intensity at high resolution due to reduction in B factors,
reduction in radiation damage, anything else?
Colin
-Original Message-
From: CCP4 bulletin board [mailto:[EMA
Hi
If you mean organic small molecules, then the opinion for the last 15
years at least is probably "yes, unless you know you'll have a phase
change".
Most small molecule crystals don't have the same problems with
needing cryoprotectants as macromolecules, due in large part to not
havin
Dear Scientists and Friends,
I am not sure, whether organic crystals need to be in cryo stream
necessarily during data collection from an in house
xray machine .
How most of the organic crystals have been solved mostly?
--
S.Jayashankar
(A bit confused new generation researcher).
Research
Dear All
there is a slim 800 lb tarball at
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99d-src.tar.gz
this is to test the build and arrangement of files.
If you want balbes you will have to manually install PyXML (run the
setup.py in PyXML-... using "python setup.py build" followed by
"python s
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