RNR complexes with 2x ATP: 8VHN, 8VHP, 8P23, 7AGJ
NrdR complex with 2x ATP: 7P37
NrdR complexes with ATP and dATP: 7P3F, 7P3Q
Apologies to anyone whose structures I inadvertently missed!
/Derek
_
Derek Logan
Professor | Biochemistry and
?
Thanks
Derek
_________
Derek Logan
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se
To unsubscribe from the CCP4BB
ally entitled to work in Sweden.
/Derek
_____
Derek Logan
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lun
Dear all,
I'd like to draw your attention to job opportunities at SARomics Biostructures
in Lund, Sweden, a rapidly growing CRO in structural biology for the pharma and
biotech sectors, based in Lund, Sweden. SARomics are looking to recruit several
scientists in protein expression and purificat
_
Derek Logan
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se
<https://lu.varbi.com/en/what:job/jobID:721686/>
[lu_logo_ogimage.png]
Doctoral student in structural
b
Posted on behalf of SARomics Biostructures AB!
Best regards
Derek Logan
Open position: Research Scientist in structural biology
SARomics Biostructures is one of the fast-growing biotech companies in Lund,
Sweden. We strive to accelerate drug discovery through structural insight. Our
Derek
_
Derek Logan
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se
###
Dear all,
Please see below for a job advertisement posted on behalf of a local company,
SARomics Biostructures (which, as a disclaimer, I have to admit to having
co-founded...)
Best wishes
Derek
_
Derek Logan
Professor | Biochemistry and
u need, but there is the interactive task of model
preparation with mrbump and ccp4mg in the bioinformatic tasks, which might
allow what you want to do.
Cheers
Christian
On Thu, Oct 15, 2020 at 11:02 PM Derek Logan
mailto:derek.lo...@biochemistry.lu.se>> wrote:
Hi all,
I'm look
Hi all,
I'm looking for some advice on MrBUMP. Is it possible to access MrBUMP via
CCP4I2 with all the options it had in CCP4I? The options seem to have been
drastically trimmed in CCP4I2. The reason I ask is that I have a tutorial that
I've put a lot of work into over the years that involves t
egards,
Jon
On Wed, 28 Nov 2018 at 16:24, Derek Logan
mailto:derek.lo...@biochemistry.lu.se>> wrote:
Hi,
I'm trying to finish off refinement of a structure I last refined in 2009, but
Refmac5 is crashing with very odd problems. I list some relevant lines from the
log files below. Esse
g for every residue in the
structure. It also complains that it doesn't recognise NAG residues that worked
perfectly fine before. I am using the exact same coordinates that worked with
Refmac5 in 2009. What can have changed?
Derek
_____
D
oming out of sync. Are you running AMPLE from ccp4i?
>
> A new ccp4 update will be released in the next few days that will hopefully
> fix the problem, but if not, please let us know.
>
> Best wishes,
>
> Jens
> ____
> From: CCP4 bull
Hi,
I've been trying to run AMPLE on Linux, but it crashes at startup with the
message:
__main__.py: error: unrecognized arguments: -use_arpwarp False
I don't know how to resolve this and have resorted to running ample from the
command line using the flags generated by CCP4I except for the off
roblem? I don't have this issue on my Mac.
Thanks
Derek Logan
Hi,
The structural biology CRO SARomics Biostructures in Lund, Sweden, has an open
position for a protein crystallographer. The application deadline is 1st
December. See here for details:
https://www.saromics.com/About/About/Career.html
Best regards
Derek Logan
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht
On 27 Oct 2017, at 13:41, Derek Logan
mailto:derek.lo...@biochemistry.lu.se>> wrote:
Hi,
This is a cross-post to ccp4bb and phenixbb. I'm trying to refine a largish
small molecule ligand. It has two confor
Dear Nishant,
Did you ever get an answer to your question? I came across it while looking
through old e-mails. This has happened to me on every Mac I have run MrBUMP on
in recent years (always in Sweden). You need to go to
/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/pyth
Hi Paul,
Thanks, that was fast! There was a small typo in the phase column labels, which
I've fixed in the attached file. Otherwise it works very well. Great that it
opens the most recently-created MTZ file by default. I'll test the other option
in due course.
/Derek
On 15 Aug 2017, at 14:36
Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology
www.cmps.lu.se<http://www.cmps.lu.se>
Cent
Hi Logan,
Thanks for this useful information. Didn't know it was possible to rejig
binaries in that way! I'm taking the liberty of cc:ing your answer to the list.
I forgot to say that this problem affected both the CCP4-distributed Coot and
an old stand-alone from Bill Scott that I had in /Libr
Hi,
I recently upgraded my Mac to Sierra (I know, early adopter...) and thereafter
the latest XQuartz (2.7.10_rc3). The latter step seemed to break Coot,
apparently because Coot requires the run-time library
/opt/X11/lib/libXt.6.dylib and this has been replaced by
/opt/X11/lib/libXt.7.dylib. I
Hi,
I would like to come into contact with users of the Formulatrix NT8, especially
if they have the LCP option. If you have one, please contact me off-list.
Best regards
Derek
Derek Logan
These last puns just take the biscuit!
Derek
On 1 Apr 2015, at 16:52, David Briggs
mailto:drdavidcbri...@gmail.com>> wrote:
This looks like a tough cookie.
IMO you'd be crackers to persist with this crystal form. It's certainly not
going to be a piece of cake.
Dr David C Briggs PhD
http://a
I believe the correct approach is k-fold statistical cross-validation, but can
someone remind me of the correct way to do this? I've done a bit of Googling
without finding anything very helpful.
Thanks
Derek
____
dish the whole thing is in English. On the same web page
there is a 20-minute programme with soundbites from Eleanor and Elspeth Garman,
but that’s mostly in Swedish. Enjoy!
Derek
____
Derek L
Hi,
I found that after upgrading to Yosemite and installing the latest version of
X11 (2.7.7), X11 was now in /opt/X11R6 rather than /usr/X11R6. In my case ccp4i
and coot both stopped working. I have no idea how the move happened, as no
options were presented during installation of X11 to put i
amp;Type=E
For further details you can also contact
Derek Logan, Senior lecturer
derek.lo...@biochemistry.lu.se
Esko Oksanen, Adjunct lecturer
esko.oksa...@esss.se
Dear Wei,
The enzyme ribonucleotide reductase can, depending on organism and class, bind
ATP as a substrate in the active site (c), as an allosteric regulator of
substrate specificity at another site (s) and as an overall activity regulator
at a third site (a)! It can also bind dATP at the seco
Dear Kay,
> Concerning usage of programs, everybody has his/her preferences, but what
> could be simpler than a 2-liner XDSCONV.INP like
> INPUT_FILE=XDS_ASCII.HKL
> OUTPUT_FILE=temp.hkl CCP4 ! or CCP4_F or CCP4_I or SHELX or CNS
> and then running XDSCONV by running "xdsconv"? At least there's
sufficient multiplicity?
But yes, pedantry aside, I will start using pointless in my csh pipelines.
Best wishes
Derek
> On 02/14/2014 03:57 PM, Derek Logan wrote:
>> Hi,
>>
>> I am a long time user of XDS (20 years this year) but all the same
>> I find that I have cons
servations have gone in and the geometric mean is
indeed output. That would put my mind to rest!
/Derek
________
Derek Logan tel: +46 46 222 1443
Associate Professor
ease a fix for this in an update
in the near future. It could be through a change to Phaser or to the log file
parsing, I don't know for sure.
/Derek
On 4 Dec 2013, at 11:42, Derek Logan wrote:
> Hi again,
>
> Following up on my mail earlier this morning, I installed CCP4 in
Hi again,
Following up on my mail earlier this morning, I installed CCP4 in a virtual
Windows XP machine on my Mac. When I run Phaser in Windows the QtRView output
is lacking the graphical section, as described for the course computers, but I
can open the log file generated in the Mac OS X vers
ed running the Phaser job directly on the server (which
has Windows Server 2003 R2) and the output is also lacking the graphs. I was
wondering if this was a known issue. I haven't found anything on the Web.
Thanks
Derek
______
m: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Derek
Logan
Sent: 24 October 2013 19:08
To: ccp4bb
Subject: Re: [ccp4bb] largest protein crystal ever grown?
Hi,
Last spring I visited the Protein Crystallography Station at Los Alamos. On a
shelf, in a capillary in a serious exh
24h exposure :-)
Derek
____
Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology www.cmps.lu
-
> Hash: SHA1
>
> Probably brighter than an XFEL if you average over a reasonable amount
> of time greater
> than fs ;-)
> Tim
>
> On 06/03/2013 05:13 PM, Jacob Keller wrote:
>> Brighter than XFEL? Or is it going to be an XFEL?
>>
>> JPK
>>
Hi,
If anyone fancies becoming Life Science Director at the world's brightest light
source, look no further than here:
http://www.lunduniversity.lu.se/o.o.i.s?id=24914&Dnr=547454&Type=E
/Derek
___
To be honest I preferred this more homespun work:
http://www.guardian.co.uk/science/gallery/2013/jan/10/research-as-art-competition-in-pictures?INTCMP=SRCH#/?picture=402066318&index=3
Somewhat reminiscent of Byron's Bender models:
http://www.umass.edu/microbio/rasmol/history.htm#bender
/Derek
A 4-year PhD position is available in the groups of Dr. Derek Logan and Prof.
Ulf Ryde at the Dept. of Biochemistry and Structural Biology and the Dept. of
Theoretical Chemistry at Lund University, Sweden. The project is sponsored by
the European Spallation Source and will also involve the
w8gOC1NSXBw&sa=X&oi=mode_link&ct=mode&cd=2&sqi=2&ved=0CBMQ_AUoAQ
>
> (all that should be on one line, or just google for "gchq" and look at the
> images).
>
> On 12 Jun 2011, at 19:55, Derek Logan wrote:
>
>> Hi everyone,
>&g
ing_suggestions/Snöhetta/MaxLab_Aerial_FINAL_II.jpg
/Derek
_______
Derek Logantel: +46 46 222 1443
Associate Professorfax: +46 46 222 4692
Dept. of Biochemistry and Structura
undulator beams at the
ESRF! There are a few free days left in our spring schedule:
http://cassiopeia.maxlab.lu.se/index/organiser-app
Good luck
Derek
___
Derek Logantel: +46 46 222 1443
Associate
___
Derek Logantel: +46 46 222 1443
Associate Professorfax: +46 46 222 4692
Dept. of Biochemistry and Structural Biology mob: +46 76 8585 707
Centre for Molecular Protein Science
www.cmps.lu.se<http://www.cmps.lu.se>
r.app/Contents/MacOS/XDS-Viewer) it
seems to work fine.
However for the diffraction image viewing I would suggest adxv. You
can find it at: http://www.scripps.edu/~arvai/adxv.html.
Andrzej
On 5/3/09 15:21, Derek Logan wrote:
Hi,
I very recently downloaded and installed the Mac OS X executab
referred shell? Looking in the XDS Viewer.app
directory I can't find any obvious clues.
Thanks
Derek
______
Derek Logan tel: +46 46 222 1443
Associate Professor fax: +
I was much more enticed by the proposition of the MacBook Wheel:
http://www.theonion.com/content/video/apple_introduces_revolutionary
Get your orders in now - there's reportedly a 3-15 month waiting time...
Derek ;-)
On Jan 6, 2009, week2, at 13:14, JBosch wrote:
Hi Sheemel,
I assume you are
density?
Thanks
Derek
__
Derek Logan tel: +46 46 222 1443
Associate Professor fax: +46 46 222 4692
Molecular Biophysics mob: +46 76 8585 707
Centre for
Hi,
Whatever happened to the Yahoo group pxrbtx (PX robotics), that was
started by Ingo Koendorfer in 2006? There haven't been any postings
since Feb. 2007. Maybe time to revive it?
Derek
On Sep 10, 2008, at 15:19, Critton, David wrote:
To the CCP4bb members who are/have been users of Art
://www.crystallographyschool.org/
The 9th International School on the Crystallography of Biological
Macromolecules
Società del Casino, Como, Italy
September 29th–October 3rd, 2008
ORGANISERS
Prof. Keith Wilson (York University, UK)
Dr. Marjolein Thunnissen (Lund University, Sweden)
Dr. Derek Logan (Lund University
Dear all,
The registration deadline for the Como Crystallography School has been
extended to 28th August. For more details see the web site http://www.crystallographyschool.org
. Please note that the deadline for booking accommodation has not been
extended from the initial date of 25th July.
*** ONLY TWO WEEKS TO GO! ***
There are only two weeks left to register for the Ninth International
School on the Crystallography of Biological Macromolecules
Como (Italy), 29th September – 3rd October 2008. The School is one of
the premier forums i Europe for dissemination of developments in
Cell
and Organism Biology and Dr. Derek Logan at the Dept. of Molecular
Biophysics, Centre for Molecular Protein Science. For more details, see:
http://mole.mbfys.lu.se/pdf/Postdoctoral_position_Aug_1.pdf
Lund University, the largest university in Scandinavia, has excellent
facilities for
;-) But hey, let's not go *there* again...
Derek
__
Derek Logan tel: +46 46 222 1443
Molecular Biophysics fax: +46 46 222 4692
Centre for Molecular Protein Science
68 uM was described as belonging to the weakest complexes solved
to date, but this article was from 1999 and much water has passed
under the bridge since then.
Thanks
Derek
_
Derek Logan tel: +46 46
- When Rontgen discovered a new kind of light, he called it "x-
rays". Now only the Germans call them Rontgen rays.
Thanks for a great essay! Since I have nothing of real value
contribute here, I won't pass over the opportunity to be a
"besserwisser" (as the Swedes say, using a borrowed wor
: 24th July
Accommodation: 25th July
Abstracts: 28th August
ORGANIZERS
Keith Wilson (York University, UK)
Derek Logan (Lund University, Sweden)
Marjolein Thunnissen (Lund University, Sweden)
PRINCIPAL FUNDING
EU Network MAX-INF2 (contract RICA-CT-2004-505977)
PRELIMINARY PROGRAMME AND REGISTRATION
The
)
Derek Logan (Lund University, Sweden)
Marjolein Thunnissen (Lund University, Sweden)
PRINCIPAL FUNDING
EU Network MAX-INF2 (contract RICA-CT-2004-505977)
PRELIMINARY PROGRAMME AND REGISTRATION
The meeting will last from after lunch (not provided) on Monday
September 29th, 2008, to after lunch
Great program by the way!
xtriage.log
Description: Binary data
2008/4/23, Derek Logan <[EMAIL PROTECTED]>:
Hi everyone,
Can anyone help me with interpretation of a self rotation function
and
native Patterson from a dataset with pseudosymmetry? I've always
been a bit
poor on sphe
Thanks to everyone who helped with the self RF problem: Eleanor, Ian,
Claudine, Pietro & Alexei.
Eleanor wrote:
1) It is a bit hard to find out how MOLREP defines its orthogonal
axes - many programs use X0 || a, Yo || b* and in P21 hence Zortho
is || to c*
If that is what Molrep does then
Hi everyone,
Can anyone help me with interpretation of a self rotation function and
native Patterson from a dataset with pseudosymmetry? I've always been
a bit poor on spherical polars. The space group is P21 with beta =
92.2°. The kappa=180° section of the SRF, calculated using Molrep, is
n the
other. Is there any convenient way to merge the projects? I guess the
answer is no, or else the question would have been asked and answered
already ;-)
Thanks
Derek
--
Derek Logan tel: +46 46 222 1443
Molecular Biophysicsfax: +46 46 222 4692
Lund University mob: +
Hi again,
Martin pointed out to me that my description of the BioRad machine was
in fact of an older model from ca. 2003 which indeed required manual
filter changes. The iQ5 has multiplexing capability just like the
Mx3005p. I'll leave further discussions to the experts ;-)
Derek
Hi Jeroen,
We just bought a Stratagene Mx3005p for the Thermofluor method (also
known as differential scanning fluorimetry). This was after talking to
Martin, among others, he he... We haven't had it long and did our
first experiments last Friday, but it produced good results straight
awa
. Is it possible to change the default values?
Thanks
Derek
--
Derek Logan tel: +46 46 222 1443
Associate professor fax: +46 46 222 4692
Molecular Biophysicsmob: +46 76 8585 707
Lund University
Box 124, Lund, Sweden
interpretable electron densities. So, I
regard this method as a very powerful alternative, where the
availability of SeMet-crystals is limited.
Best regards,
Uwe
Derek Logan schrieb:
Hi,
I'd like to find out how successful the "quick soak" method for
heavy atom derivatisation pro
will necessarily be anecdotal, but let's not let that stop us.
Derek
--
Derek Logan tel: +46 46 222 1443
Associate professor fax: +46 46 222 4692
Molecular Biophysicsmob: +46 76 8585 707
Lund University
Box 124, Lund, Sweden
2:01 +0200
Derek Logan <[EMAIL PROTECTED]> wrote:
Hi,
I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10
using
the binary installer from the automatic download page. Everything
works fine and dandy except xplot84driver. This currently means I
have
ile format" and does not open the plot file. Does
anyone have an idea what is going on?
Thanks
Derek
--
Derek Logan tel: +46 46 222 1443
Molecular Biophysicsfax: +46 46 222 4692
Lund University
Box 124, Lund, Sweden
Pedant's corner:
The systems are actually called ÄKTA (loosely "the real thing" in
Swedish") and not AKTA ("watch out!", "beware!"), although given the
feelings expressed about the price, the latter may not be such a
misnomer ;-)
Phew, I got th
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