Dear all,
If you have any promising undergraduate or masters level students I would be
grateful if you could point them to the following, funded, PhD opportunity in
my laboratory. They are welcome to send me an email for an informal chat prior
to an application.
"Molecular basis of C-reactive
If it helps an academic colleague of mine has been developing hi-res
full-colour 3D printed molecule models for the last 6 months or so and is very
happy to help design and make any molecules of interest. These can include
mini-magnets to click pieces together (ligand binding etc). I’ve included
Dear colleagues,
A number of PhD bursaries have become available at my institution. I would be
grateful if you could direct any UK/EU students who might be looking for such
opportunities to the following link:
http://www.port.ac.uk/postgraduate-research/funding/phd-biomedical-and-biomolecular/
Posted on behalf of a colleague:
Opportunity for Object-Recognition and Augmented Reality Programmer:
- University of Portsmouth
- Six-month Postdoctoral Research Fellow, Grade 7 (spine-point 35)
- £18k for 6 months
- Starts 5th January 2015
- Based in the School of Creative Technologies, in coll
Hi all,
Thanks for your help.
CORRECT.LP includes precisely the information I was after.
Also Ian Tickle’s article on http://www.ccp4.ac.uk/html/alternate_origins.html
is very helpful.
Simon
Dear ccp4bb,
Could someone either provide, or point me to, a list of space-groups relevant
to protein crystallography just by space group number? I can find lots of
tables that list them by crystal system, lattice etc. but no simple list of
numbers.
Thanks,
Simon
following link (job
reference 10012179 under external vacancies (EU only)):
https://port.engageats.co.uk
Closing date is 27th July with interviews aimed for 11th August. I am happy to
be contacted informally for further information.
Thanks!
Simon
--
Dr. Simon Kolstoe
Institute of Biomedical
Hi there,
I've got a text file with multiple conformations of a ligand that has been
docked to a protein using autodock, which I am trying to split into separate
pdb files in order to visualise in pymol/coot etc.
Previously I've used the script pasted below, but it is now falling over just
aft
I am routinely having the Mac vs Linux conversation with crystallographers and
new students, especially given the price of Macs.
Generally I think that the extra money spent on a Mac pays for less time spent
messing around installing software, sorting out dependencies, swearing at the
less than
Dear ccp4bb,
About 6 years ago I noted a couple of structures I was interested in were
removed from the pdb. I saw in a recent email discussion that it is possible to
access obsolete entries, however unfortunately I do not have the pdb code of
the structure I am interested in - and neither does
Dear ccp4bb,
One of my colleagues is interested in how a certain protein differs between
species. He's done a blast search, collected all the aligned sequences, and
"emailed them to the crystallographer to tell him the implications of the
sequence changes".
Although I am not at all confident
Dear ccp4bb,
I am quite a fan of XDS and have just upgraded to the latest version.
Normally, to assess the quality of my data, I look at the tables in
CORRECT.LP and especially the table "SUBSET OF INTENSITY DATA WITH
SIGNAL/NOISE >= 0.0 AS FUNCTION OF RESOLUTION".
However in my latest ru
Dear CCP4bb,
I've just started on a new project and was rather excited to see
protein spots for my first few crystals at Diamond the other day. The
only problem is that the reflections only went out to 8.5A. As it
should be possible to get a solution using molecular replacement (and
whils
One of my colleagues asked if I could post the following to the ccp4bb:
Thanks to very helpful feedback, there is now a fairly comprehensive
set of curations for the new 'Crystals, X-rays and Proteins' (Sherwood
and Cooper) at the following link:
http://www.ucl.ac.uk/~rmhajc0/
The first 6
appropriate to draw these conclusions?". It is whilst asking these
two questions that rules of thumb become somewhat handy, especially
when they coincide with the rules of thumb used by the referees.
Simon
On 28 Oct 2010, at 10:28, Eleanor Dodson wrote:
Oh cynic!
Eleanor
On 10/27/2010
Surely the "best" model is the one that the referees for your paper
are happy with?
I have found referees to impose seemingly random and arbitrary
standards that sometime require a lot of effort to comply with but
result in little to no impact on the biology being described. Mind you
disc
Dear all,
What's the best way to convert a coordinate cif file to a pdb (without
compiling a program, installing new utilities, writing script files...)?
Cif2mtz works for the reflection file however coordconv doesn't have a
"cif" option. If I try using Coot I get a mangled pdb file that gi
, F.Xavier Gomis-Rüth wrote:
Could you please let us know when it appears ?
A message to the ccp4bb would be really very much appreciated.
Best,
Xavier
Simon Kolstoe escribió:
FYI an updated version of the Sherwood book will hopefully be
published in the next few months.
Simon
On 10 Jul 2
FYI an updated version of the Sherwood book will hopefully be
published in the next few months.
Simon
On 10 Jul 2010, at 18:04, Vineet Gaur wrote:
Hi,
I found "Crystal, X-rays and Proteins" by Dennis Sherwood very
helpful in understanding the basic concepts of crystallography.
However,
Dear CCP4bb,
I am still playing around scaling two datasets together and have
noticed another interesting behavior in scala. If I scale all my data
(from 1.5A to 51A) I get 100% completeness in my outer shell, 98% in
my inner shell and 99.9% overall, stats that I am normally quite happy
w
f you want: this is not
normally recommended since they are pretty inaccurate (look in the
"Excluded data" tab of ccp4i/Scala)
If you are merging strong & weak datasets it should do the right
thing, I think.
Phil
On 7 Jun 2010, at 15:09, Simon Kolstoe wrote:
Dear CCP4bb,
I
Dear CCP4bb,
I was wondering if someone could tell me how mosflm and scala deal
with overloaded reflections. From my understanding mosflm extrapolates
the overloaded peaks but then scala throws them out completely - is
this right?
If so am I right to not worry about "contamination" from e
Thank you ccp4bb for guidance once again, and especially Jurgen Bosch
for suggesting Voidoo and Oliv Eidam for suggesting Dockblaster.
I was able to use Voidoo which I already had installed from USF to
better define the cavity I was interested in. I then was able to use
the free web server
Dear ccp4bb
A structure I have recently finished has a cavity with four waters in
it. I am wondering if I might be able to fit a small molecule in the
same place. Does anyone know a way of making some type of map of this
cavity and then searching through a small molecule library to see what
Hi,
I have 20 identical monomers in my asu of a 2.5A structure. We have
previously model built all twenty monomers and used strict NCS in the
refinement, however I would like to compare this with the maps generated by
building one monomer into an averaged map and then replicating it nineteen
ti
Hi Fred & Seb,
It might be slightly different in France, however in the UK a basic
education in science is one of the best career steps someone can take
(up to degree level). Granted staying in academic research is not as
easy as moving into industry, but in the schools work I have done I
But pomo only descends so far in science - by the time you get to
crystallography you are back into pre-modern religion - the R gods!
Simon
On 7 Oct 2009, at 09:56, Kevin Cowtan wrote:
William G. Scott wrote:
On Oct 6, 2009, at 1:32 AM, Morten Kjeldgaard wrote:
teleports the students acr
Dear all,
In the phaser .sol file what do the two LLG's correspond to on the
SOLU SET line eg
SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821
Do they show an initial and a refined LLG or do they correspond to the
rotation and translation function as in the Z scores?
I checked the app
Hi Todd,
I've found, in two institutions I have now worked for, that the
tradeoff is between IT support and the hardware/software you want to
use. When our group moved institutions recently our new IT department
told us that they would only support managed desktops on windows
machines. We
It's also easier to fish the crystals out of the solution with a
hanging drop.
Simon
On 1 May 2009, at 06:35, Debajyoti Dutta wrote:
Hi,
>From the experiance of mine I can tell you that the crystal size
sometimes matters between these two methods. Hanging drop may yield
bigger crysta
Thanks to Robbie Joosten who suggested updating to refmac 5.5.0090
which seems to be happy with alternate conformation again.
I thought it was probably worth mentioning on the list that the ccp4
bundled refmac has this bug.
Simon
On 17 Apr 2009, at 14:07, Simon Kolstoe wrote:
Dear
Dear ccp4bb,
I've finally gotten around to updating my ccp4 to version 6.1.1 with
the default refmac 5.5.0072 that comes with this from the ccp4
downloads site. I am working on relatively high resolution structures
with a number of alternate conformers for certain amino acids which I
put
Dear ccp4bb,
Thanks for the help. To summarise:
1) CCP4's tcl/tk installs into /usr/local/X11/bin
2) To point imosflm to this version of Tcl/Tk the line "export
MOSFLM_WISH=/usr/local/X11/bin/wish8.4" needs to be in a file
called .bash_profile NOT .profile for some reason (but not if you ar
Dear ccp4bb,
I'm trying to update Tcl/Tk on a mac running OSX5.6 as my version of
mosflm has suddenly started crashing when trying to autoindex, so I
figured the best thing to do was to reinstall both mosflm and its
dependencies.
So I went to the CCP4 download page and used the Daresbury
Dear ccp4bb,
Can anyone point me to a table/paper that gives "acceptable" RMSD's
for bond lengths and angles against resolution? We have had two
different referees for a paper contradict each other and I am not sure
what to use as a good authority for this.
Thanks,
Simon
I've gone off computers completely after finding that if I stare hard
enough at my diffraction pattern I can sketch the density by hand :-)!
Actually it's OSX for me because I view myself as a scientist who uses
computers rather than a computer expert who uses science. Linux is
just that bi
Hi,
I'm trying to install pointless on OSX.5 I've downloaded a working
binary to my ccp4/bin directory however everytime the program runs (on
the command line) I get:
Environment variable SYMINFO not set ... guessing location of symmetry
file.
Environment variable CLIBD not set ... big t
Hi Louise,
Update your Xquartz with:
http://xquartz.macosforge.org/trac/wiki/X112.2.3
then every time you get an apple update make sure it doesn't re-
install the earlier version!
Simon
On 14 Jul 2008, at 08:44, Louise Gourlay wrote:
Dear All,
I have a Mac OS X Leopard operating system
Hi,
I am trying to process data with the new XDS version (June 2nd)
however the new space group determination sub-routine is picking the
wrong space group. Can I simply run CORRECT after the INTEGRATE step
as in the old version putting in the space group I want? If so is
there no longer n
Dear ccp4bb,
I have heard from many people that molprobity is the gold standard as
far as validation is concerned. As I am just about to deposit a
structure I therefore figured it was best to use molprobity in guiding
the final stages of my refinement. I do not have enough data to
justify
I co-crystalise a protein with insoluble ligands fairly frequently and
normally dissolve the ligand (about 1mg) in 50ul DMSO and then add
450ul buffer. The solution is often rather cloudy so I set up one set
of hanging drops with the cloudy solution, then spin out the
precipitate and set up
Has anyone found a solution to the X window problem on macs running
10.5.2? Both Coot and pymol are becoming almost unusable by freezing
frequently because of X11 "not responding". I've upgraded my X11 to
2.1.4 from the webpage http://trac.macosforge.org/projects/xquartz/
wiki/ but the probl
L, I'm not sure what phenix.refine does.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Wed, 12 Mar 2008, Simon Kolstoe wrote:
Dear CCP4bb,
I was l
Dear CCP4bb,
I was looking through the REFMAC manual today and found the following
advice:
"Completing the data to include all possible hkls. Should do this
after data reduction, and certainly before using REFMAC. This is now
done with the uniqueify script. It is best done using CCP4i."
wrong.
Simon
On 21 Feb 2008, at 17:32, Michele Lunelli wrote:
Simon Kolstoe wrote:
I converted the resulting XDS_ASCII.HKL using xdsconv and then
f2mtz ready for phaser and refmac.
Sorry if this is obvious, but you should also run CAD after f2mtz,
as reported at the end of the log file
s in many cases essential.
Best regards,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
Of Kay Diederichs
Sent: Thursday, February 21, 2008 3:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] XDS and overlaps
Simon Kolstoe schrieb:
Whilst w
Whilst we are on the subject of XDS...
I had difficulty processing a data-set in mosflm the other day so on
the recommendation of a colleague switched to xds which, with a bit of
tweaking, seemed to work really well. I converted the resulting
XDS_ASCII.HKL using xdsconv and then f2mtz ready
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