Hello All,
Just wondering if anyone else is having issues with Coot crashing (regularly,
not just once in a while).
I get the following error message:
/home/pea246/bin/ccp4-7.0/bin/coot: line 318: 2025 Segmentation fault
(core dumped) $coot_bin "$@"
guile (GNU Guile) 2.2.3
Packaged by
Hello Chandra,
Soaking heavy atoms into crystals has a long and successful history (I use it
pretty often and it works much of the time). If you need phase information and
you have some crystals, I would certainly give it a try. There are many papers
and books to give you methods to do this
than the one 'optimal' condition.
Best regards, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
From: CCP4 bulletin board on behalf of Markus Heckmann
Sent
, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent:
?We have some crystals that diffract well when fresh (less than one week old)
but lose almost all diffraction by the end of 2 weeks, so age can matter. One
crystals are in liquid nitrogen, they should be safe from further degradation,
but may suffer from ice contamination.
cheers, tom
Tom
I think all of those numbers would be pretty acceptable to almost all referees
;-)
Cheers, tom
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Deepali
Verma
Sent: Tuesday, 5 June 2018 7:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Acceptable range of CC1/2
Dear all,
?
Best of luck, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
From: CCP4 bulletin board on behalf of Liuqing Chen
<519198...@163.com>
Sent: Monday,
Unfortunately it is unlikely that the costs for robotic equipment (at least the
larger scale equipment) will come down much.
It is effectively all ‘bespoke’ equipment and will never benefit from high
volume manufacturing (nothing like phones or cars).
How many crystallisation centres are needed
I agree with Tristan, it can be quite easy to crystallise a contaminant even
when one is trying to be careful during the purification process.
Before everyone had a mass spec, looking at gels didn't tell you as much as you
needed to know, as many proteins don't stain well, so are hard to see on
Hello All,
I would second the notion that transient systems are quite good for testing
expression levels on the small scale and can be used for scale up (to a certain
degree at least). It is probably the fastest way to go to screen a number of
constructs.
Cheers, tom
-Original
A lot of plant genomes are big- wheat for example is 12 Gb, so it may not be
quite as trivial as one might expect.
cheers, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
Dear Board Readers,
For anyone who might be interested, or know of interested persons, there is a
postdoctoral position available at CSIRO:
https://career10.successfactors.com/sfcareer/jobreqcareer?jobId=39270=CSIRO
Best regards, tom
on the stability of the protein. ?We also
saw this was consistent across multiple space groups. If you would like to have
a look, they were just released: 5HY0, 5HY2, 5HY4.
As a comparison to another protein in this fold class that doesn't have the
disulfide is 5HWE.
cheers, tom
Tom Peat
Proteins
I don't know about Europe, but it is very tight Down Under...
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William
G. Scott
Sent: Wednesday, 9 November 2016 4:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] just out of totally idle
I think the more interesting questions are: should one want to disrupt such a
tight interaction?
Wouldn’t the structure of the protein bound to DNA be more interesting than the
protein alone?
Why not try to crystallize the complex and show how the protein binds?
Sometimes you should just run
their
software after others have gone in and modified it, which is unrealistic.
I just think it is unrealistic to expect the source code just because someone
wrote a paper (again, I like open source, but not everything is destined to be
open source).
cheers, tom
Tom Peat
Proteins Group
Biomedical
Hello All,
I am appealing to the community as I don't seem to be able to find through
Google what I am looking for, and I just don't have the ability to look through
every structure in the PDB to find this.
I have what I think is an interesting case: a two domain protein structure with
a
but more so for acidic residues. See HIV protease Asp-Asp
as a well-established example
Hope this helps
J
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: Friday, 28 March 2014 12:12 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb
throughput).
Good luck, tom
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bosch, Juergen
[jubo...@jhsph.edu]
Sent: Tuesday
. When I
took a guess by putting in the 'MolProbity score' I was basically called an
idiot that can't follow directions. Help on this front would be appreciated as
although I have been called worse things, it would be nice to eventually get
what is being referred to.
Thanks, tom
Tom Peat
CSIRO
Slightly off the topic, but still potentially relevant in terms of realistic
experimental error: when dealing with the small volumes typically used in
crystallization (say 1 uL + 1 uL drops), and using a 10 uL pipette, the errors
are fairly high (more like 30% than 5-10%), leading to a lot of
A chip in my brain to remember all of the things I should know/remember would
be very convenient if we are really talking about having a good memory system.
It means it would also be easier to extract that personal perspective and pass
it on.
Cheers, tom
From: CCP4 bulletin board
The following could be of use:
Newman, J. Expanding screening space through the use of alternative reservoirs
in vapor diffusion (2005) Acta Cryst D61(4), 490-493
Cheers, tom
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix
Frolow
Sent: Tuesday, 13 November 2012
this notion originated from.
Cheers,
Tim
On 04/03/12 22:07, Tom Peat wrote:
We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work
fine on this.
I can't say I notice a big performance boost from the 64 bit side of things.
Maybe I'm just impatient.
cheers, tom
Tom Peat
We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine
on this.
I can't say I notice a big performance boost from the 64 bit side of things.
Maybe I'm just impatient.
cheers, tom
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville, VIC, 3052
+613 9662
(at least in many ways).
I would be happy to give my name when reviewing, as I feel it is my job to
improve the paper, and I can still face my colleagues after the exercise.
cheers, tom
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
Bernard went to a lot of work to verify that this structure was wrong, so we
should also thank him for his efforts.
It is good to see someone who has a hunch follow that up and let the rest of us
know about it.
Thanks Bernard!
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville
If you find yourself in the situation where the buffer you started with is out
of range of the pH you would
like to attain, there are sets of buffers you can use that contain most of the
standard buffers that will give
you a fairly linear response across ~4-10, as described by Newman, Acta
To elaborate further on software packages available that do a reasonable job of
fitting small molecules and outputting reasonable dictionaries, one could
consider Afitt from OpenEye Scientific Software. They have academic as well as
commercial licenses to their software.
Cheers, tom
You might to consider that PEG 3350 has phosphate contamination, so playing
around with small amounts of phosphate (or removing it) might be worthwhile.
Cheers, tom
From: Regina Kettering [mailto:reginaketter...@yahoo.com]
Sent: Thursday, August 25, 2011 04:46 AM
To: CCP4BB@JISCMAIL.AC.UK
I took a quick look via Google and in the FAQ to see if there was anything on
this topic, but didn't find the clue I was looking for.
I just installed version 6.2.0 on a linux box running Centos 5.6 and I get
error messages every time I try to read in a mtz file- unreadable. I check the
file
Hello All,
It turns out that the /tmp directory being used by ccp4i had incorrect
permissions, which gave rise to the problem. Thanks for the solution!
Cheers, tom
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: Thursday, 21
Hello-
Sorry to be disagreeable, but I think it depends on the protein. We've had
much better success in getting reproducible crystals when we've snap frozen in
liquid nitrogen in small aliquots (thin walled PCR tubes work best). We can
then screen and optimize using the same protein prep-
Hello again,
I still think it depends on the protein complex, but I agree that the
consensus/ hearsay/ anecdotal/ old crystallographer's tales revolve around
complexes not working as well as single proteins for freezing. I'm not sure
that has been shown to be the case, although again I would
://www.csiro.au/org/CMHT.html
Questions can be directed to me (Tom Peat) at the following email address:
tom.p...@csiro.au
We seek an enthusiastic and highly motivated protein crystallographer to
join the Structural Biology research group in Parkville. You will be
responsible for protein
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