[ccp4bb] Job opportunity at SARomics Biostructures in Lund, Sweden

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

[ccp4bb] Research engineer position at Lund Protein Production Platform

_ Derek Logan Professor | Biochemistry and Structural Biology Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden www.cmps.lu.se

[ccp4bb] Industrial crystallographer position in Lund, Sweden

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

Re: [ccp4bb] MrBUMP in CCP4I2

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 looking for

[ccp4bb] MrBUMP in CCP4I2

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

Re: [ccp4bb] Refmac5 crashes with coordinates last refined in 2009

n 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. Essentially re

[ccp4bb] Refmac5 crashes with coordinates last refined in 2009

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 _ Derek Logan

Re: [ccp4bb] Unrecognised argument problem in AMPLE

coming 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 bul

[ccp4bb] Unrecognised argument problem in AMPLE

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

[ccp4bb] Problems with QT graphs in Aimless log files

this issue on my Mac. Thanks Derek Logan

[ccp4bb] Crystallographer position at SARomics Biostructures

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

Re: [ccp4bb] Refining alt. confs for only part of a ligand

l Researcher Lab of Piet Gros Crystal & Structural Chemistry Group Universiteit Utrecht On 27 Oct 2017, at 13:41, Derek Logan <derek.lo...@biochemistry.lu.se<mailto:derek.lo...@biochemistry.lu.se>> wrote: Hi, This is a cross-post to ccp4bb and phenixbb. I'm trying to refine a la

Re: [ccp4bb] MrBUMP error

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

Re: [ccp4bb] [phenixbb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

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

[ccp4bb] Opening phenix X-ray/neutron maps in Coot without the Phenix GUI

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>

Re: [ccp4bb] Latest XQuartz upgrade breaks Coot

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

[ccp4bb] Latest XQuartz upgrade breaks Coot

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.

[ccp4bb] Formulatrix NT8

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

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

These last puns just take the biscuit! Derek On 1 Apr 2015, at 16:52, David Briggs drdavidcbri...@gmail.commailto: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

[ccp4bb] Cross-validation when test set is miniscule

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 Derek Logan

[ccp4bb] Eleanor interview on Swedish radio

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 Logan

Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

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

[ccp4bb] PhD position in structural biology at Lund University

details you can also contact Derek Logan, Senior lecturer derek.lo...@biochemistry.lu.se Esko Oksanen, Adjunct lecturer esko.oksa...@esss.se

Re: [ccp4bb] 2 ligands/monomer

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

Re: [ccp4bb] What really happens in XDSCONV?

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 not

[ccp4bb] What really happens in XDSCONV?

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 mob: +46 76 8585 707 Dept

Re: [ccp4bb] What really happens in XDSCONV?

. 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 constant angst about losing observations because I don't understand what goes in in the conversion steps to get to CCP4 format. I used

Re: [ccp4bb] Follow-up: Phaser output in QtRView under Windows XP

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 derek.lo...@biochemistry.lu.se wrote: Hi again, Following up on my mail earlier this morning, I installed CCP4

[ccp4bb] Phaser output in QtRView under Windows XP

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 Derek Logan

[ccp4bb] Follow-up: Phaser output in QtRView under Windows XP

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

Re: [ccp4bb] largest protein crystal ever grown?

@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 exhibition-quality glass dome, was a crystal

Re: [ccp4bb] largest protein crystal ever grown?

Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se Centre for Molecular

[ccp4bb] MAX IV Life Science Director position

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=24914Dnr=547454Type=E /Derek Derek Logan

Re: [ccp4bb] MAX IV Life Science Director position

MESSAGE- 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 On Mon, Jun 3, 2013 at 10:36 AM, Derek Logan derek.lo

Re: [ccp4bb] Coot's hidden talents!

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=402066318index=3 Somewhat reminiscent of Byron's Bender models: http://www.umass.edu/microbio/rasmol/history.htm#bender /Derek

[ccp4bb] Ph.D. position at Lund University

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

Re: [ccp4bb] off-topic: Synchrotron look alike

/Snöhetta/MaxLab_Aerial_FINAL_II.jpg /Derek ___ Derek Logantel: +46 46 222 1443 Associate Professorfax: +46 46 222 4692 Dept. of Biochemistry and Structural Biology mob

Re: [ccp4bb] off-topic: Synchrotron look alike

, or just google for gchq and look at the images). On 12 Jun 2011, at 19:55, Derek Logan wrote: Hi everyone, The latest update on the Apple story is that they are actually going to build their new headquarters in Southern Sweden: http://www.maxlab.lu.se/media_press/research

Re: [ccp4bb] Dehydration treatments

the 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

Re: [ccp4bb] AMP-PNP Hydrolysis

___ 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.sehttp://www.cmps.lu.se Lund

[ccp4bb] XDS Viewer

Viewer.app directory I can't find any obvious clues. Thanks Derek __ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics

Re: [ccp4bb] XDS Viewer

/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 executable

Re: [ccp4bb] Mac pro

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

[ccp4bb] Invisible but intact disulphides?

in the 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

Re: [ccp4bb] Art Robbins Phoenix User Group

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

[ccp4bb] Como Crystallography School registration deadline extended for the last time!

://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

[ccp4bb] Registration deadline for Como Crystallography School extended

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

[ccp4bb] REMINDER: Ninth International School on the Crystallography of Biological Macromolecules

*** 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

[ccp4bb] Postdoctoral position at Lund University

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 structural

[ccp4bb] Weakest protein-protein complex crystallised: summary

;-) 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 mob

Re: [ccp4bb] Friedel vs Bijvoet

- 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

[ccp4bb] Weakest protein-protein complex crystallised

of 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

[ccp4bb] REMINDER: Ninth International School on the Crystallography of Biological Macromolecules

: 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

Re: [ccp4bb] Help with pseudosymmetry problem

! 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 spherical polars. The space group is P21

[ccp4bb] Help with pseudosymmetry problem

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

Re: [ccp4bb] Help with pseudosymmetry problem

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

[ccp4bb] Merging CCP4i projects from two computers

on 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: +46 76

[ccp4bb] Thermofluor again

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

Re: [ccp4bb] Thermofluor

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

[ccp4bb] Default contour levels for SRF in Molrep

. 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

[ccp4bb] Quick soak method

, 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

[ccp4bb] xplot84driver problems

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

Re: [ccp4bb] xplot84driver problems

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 to convert every plot

Re: [ccp4bb] AKTA prime

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 there before Gerard! Derek -- Derek Logan