Dear All,
I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did
the "Merge Molecules" and did the refinement. In output PDB file the chain ID
sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM
numbering is starting from ligand (Chain B inst
Hi Andre,
Majorie Harding wrote a few nice papers on metal ion binding sites and their
associated coordination geometry, examples are:
Harding MM (2006) Acta D vol. 62 pp. 678-82 or Harding MM (2004) Acta D vol. 60
pp. 849-59
Best
Marc
Dr. Marc Kvansakul
Laboratory Head, NHMRC CDA Fellow
Dep
Dear all,
A postdoctoral position is available in the Wellcome Trust Centre for Cell
Biology, University of Edinburgh, for combined
crystallographic and biochemical studies of microtubule associated proteins and
molecular motors. The advert is
below and applications can be made online until May
On the whole, however, I have not seen any significant performance
advantage of 64 over 32 bit running crystallography programs
side-by-side on equivalent hardware. I have also been unimpressed with
the supposed "memory access" advantages of 64 bit. I had to do a LOT of
recompiling programs i
Hi
This is what I do:
Validate>Highly coordinated waters
From: Andre Godoy
Sent: Friday, April 13, 2012 3:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Good way to check ion sites on Coot
Dear all.
can someone tell me what is the best way to check for ion binding sites on my
structu
No, that's a limit set by the ubuntu 32 bit kernel maintainers when
they configured and compiled the kernel (again, see my comment about
the problem being with developers and users). I think the limit is 256
for x86, 4096 for ia64 (itanium), even old versions of RHEL supported
16 and 32 logical CPU
On Apr 13, 2012, at 1:24 PM, James Holton wrote:
> I tried downgrading the operating system to 32-bit, but that reduced the
> number of "CPUs" available in the system from 24 to 8. Still don't know why
> that is
I'm probably wrong, but I'll guess that a 32 bit operating system can only
spar
Dear all.
can someone tell me what is the best way to check for ion binding sites on my
structure?
I mean, a text with coordination examples, or maybe a tool on coot for it ...
best wishes
Andre
> I tell you. Technology just doesn't work.
developers and user's don't, technology is usually ok, but I feel your pain.
I myself recently had the misfortune of trying to get a java program
relying on the (apparently 32-bit only) "JMF" package to run on 64-bit
linux. This wasted almost an entire week of my life! I tried
downgrading the operating system to 32-bit, but that reduced the number
of "CPUs" available
a recent experience in our lab with molecular replacement (wt and
disordered point mutant; same space group and unit cell)
was solved with a combination of two methods.
1. We made omit maps in the disordered region at several lower
resolutions. The region became interpretable after suffereing th
Francis,
I think in the cases you describe the region in question is disordered.
Time and time again I have users coming to my beamline wanting to clean
up a "questionable region" by getting experimental phases. Ahh! If
only I had a nickle for each one. Oh wait, I suppose I kind of do? I
The laboratory of Dr. Yoonsang Cho in the Department of Biochemistry
and Molecular Biology at Saint Louis University School of Medicine
invites a highly motivated and creative postdoctoral fellow who is
enthusiastic to study ligand-receptor systems involved in inflammatory
diseases and cancer. The
Considering myself a meso-dinosaur,
I would suggest to simply grow your crystals in capillaries and then wick off
the liquid and shoot them like this without much handling.
A very efficient and simple trick is to stick a capillary in an Eppendorf tube
with the lid on using the Eppendorf tube as
Hi Prem,
In addition to other remarks made:
- You could dissolve one or more crystals in water and have mass spec done to
verify that your crystals are a complex. It takes many crystals (20-30) to make
sure on an SDS-PAGE. You will probably need to silver stain the gel to enhance
the sensitivit
> - Find a dinosaur from my generation who can suck one into a capillary and
> check diffraction at room T.
> - Try to find conditions where the crystals don't start to redissolve while
> you mount them
As a matter of fact, people begin to forget that capillaries are good not only
for checking t
Dear all,
Do you know is anyone still using Rigaku R-axis IIC X-ray diffraction
system with support services? It seems Rigaku no longer support this
systems.
Thank you in advance.
Best Regards,
Leong
"A" works as described but "t" is better!
In coot 0.6.2 I added the line
(add-key-binding "Triple Refine" "t" (lambda () (manual-refine-residues 1)))
to the file
~/.coot-preferences/coot-preferences.scm
Many thanks
Petra
From: CCP4 bulletin board [CC
I'd suggest:
- Find a dinosaur from my generation who can suck one into a capillary and
check diffraction at room T.
- Try using those loops that look like miniature tennis paddles to give the
crystal a little more support
- To minimize strain on the crystal when pulling it out of the drop, tr
Hi Paul,
You saw the wwPDB/CCDC JPG in my PPT at GSK :-)
Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means,
amongst a number of other things, that wwPDB will be allowed to use Mogul in
its validation pipeline and that wwPDB will be allowed to incorporate and
redistribute
Hi Paul,
What you might be remembering is the following paragraph from our Validation
Task Force report:
"The Cambridge Crystallographic Data Centre (CCDC) has recently entered into
collaboration with the wwPDB partners. As part of the agreement, wwPDB will
have access to Mogul, which will be
Hi Prem,
The first thing I would do is to make certain that you really have prot+DNA
crystals, and not DNA alone. If you can isolate enough crystals (you may need
15 or 30, depending on how large they are), SDS page would be informative. Run
protein and DNA alone and together in the same gel as
On 13/04/12 14:30, Tim Gruene wrote:
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Hash: SHA1
Hi Paul,
you are not referring to Gerard Bricogne's announcement for the
grade-server, are you?
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg25770.html
:) No.
If not - what type of agreement do you ha
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Hi Paul,
you are not referring to Gerard Bricogne's announcement for the
grade-server, are you?
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg25770.html
If not - what type of agreement do you have in mind?
Tim
On 04/13/12 15:14, Paul Emsley
I remember reading somewhere (or maybe at a seminar presentation?) of an
agreement between the wwPDB and the CCDC.
I can't find a reference to it on the web - is there such a thing?
Thanks (even lmgtfy answers happily received),
Paul.
Dear all,
We have a postdoctoral position available for a talented and highly
motivated individual to undertake single molecule microscopy studies on
bacterial DNA replication and DNA repair. The lab focuses on the
structural aspects of DNA replication and translesion synthesis DNA
repair, us
Are you trying to use the standard key binding "a" refine with auto-zone?
Mine does not work whilst others such as "m" and "n" for zooming out and in do.
For "a" I get the following message in the terminal:
(graphics-general-key-press-hook 97)
Key 97 not found in (scheme) key bindings
Any ideas
Hi Zhen,
I also had problems with low amounts of plasmid from yeast using 5 ml o/n
cultures. But when increasing the culture volume it worked:
Large-scale (0.51 l for obtaining preparative plasmid amounts) overnight
yeast cultures were harvested, washed in cold water once, and then
resuspended i
Dear Chris
Are you trying to use the standard key binding "a" refine with auto-zone?
Mine does not work whilst others such as "m" and "n" for zooming out and in do.
For "a" I get the following message in the terminal:
(graphics-general-key-press-hook 97)
Key 97 not found in (scheme) key bindings
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