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

[Derek Logan]

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 
international team of over 25 researchers covers the following fields of 
expertise: protein engineering, expression, purification and characterization, 
biophysical screening, protein NMR analysis, protein X-ray crystallography, and 
computational chemistry. SARomics has built a global reputation for its 
structural biology platform and structure-based drug design skills and is 
currently supporting mainly international clients in pursuing their drug 
discovery objectives. In parallel, the company is pursuing several internal 
drug discovery projects to discover leads for new medicines.

We seek skilled and highly motivated research scientists to expand and 
strengthen our team, which works on protein production and crystallization. The 
candidate can either have strong protein expression and purification skills or 
have some competence in protein production and crystallization. While not 
necessary, having competencies in both areas will be considered an advantage. 
The position involves working closely with an experienced team of 
interdisciplinary researchers and regularly presenting findings to the project 
team, senior management, and clients.

The ideal candidate will be self-driven, resourceful, organized, focused, 
service-minded, and enjoy working in a dynamic, fast-paced team environment. 
The candidate should have a strong desire to learn new techniques, incorporate 
new methodologies into their work, and carry out innovative and high-quality 
research to answer challenging questions in structural biology.

Successful candidates' requirement
• Ph.D. in biochemistry, biotechnology, molecular biology, structural biology, 
or related fields
• Experience in independent planning and performing of experiments and 
analyzing and drawing conclusions from generated data in a scientific research 
setting
• An understanding of protein structure and biophysical properties
• Have excellent analytical, organizational, and communication skills - fluency 
in English (spoken and written) is expected
• Ability and desire to work in a fast-paced, dynamic environment to ensure 
timely progress in customers' projects
• Legally authorized to work in Sweden

Required knowledge, skills, and abilities

For protein production
• Expertise in recombinant protein expression in E. coli, insect, and mammalian 
cells
• Expertise in recombinant protein purification using affinity chromatography, 
IMAC, SEC, IEX, etc.
• Working knowledge and practical experience with ÄKTA systems will be highly 
advantageous
• Expertise with general protein characterization techniques such as SDS-PAGE 
gel, Western blot, thermal shift assays, etc.

For crystallization
• Experience of protein crystallization of a wide variety of proteins
• Experience in all steps of structure determination (including data collection 
to refinement)
• An ideal candidate will also have experience with structure-based design and 
drug discovery projects

The successful candidate will get the opportunity:
• to join an energetic and enthusiastic international team with a focus on 
scientific excellence and teamwork
• to evolve in a highly multidisciplinary environment and thus develop new 
competencies outside their core expertise
• to accelerate discovery through structural insight

Explore our website to find out what it is like to work at SARomics 
Biostructures: http://www.saromics.com/
Please call Nadia Rose (+46 46 26 10 474) for specific questions regarding the 
positions.

If you are interested in a career with us, please forward a CV/resume and a 
cover letter to i...@saromics.com and label your message with the subject "SBX 
Career" no later than February 18th, 2024.

We will interview candidates continuously and would therefore like to receive 
your application as soon as possible!
The application should be in English.












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[ccp4bb] Research engineer position at Lund Protein Production Platform

[Derek Logan]

Dear all,

Lund Protein Production Platform (LP3) is a cross-faculty center of Lund 
University for protein production, characterization, crystallography and 
structure determination. It is a node within the national research 
infrastructure Protein Production Sweden (PPS) and collaborates closely with 
researchers from the MAX IV laboratory and the European Spallation Source 
(ERIC) through e.g. the MAX IV FragMAX and ESS DEMAX platforms. LP3 are looking 
for a research engineer skilled in all the above methods.

See here for details:

In Swedish: https://lu.varbi.com/se/what:job/jobID:663647/
In English: https://lu.varbi.com/en/what:job/jobID:663647/

The deadline is 17th November.

A recent survey showed that Lund is the town in Sweden whose inhabitants are 
most likely to speak positively about it to others. At least that's what our 
local newspaper reported :-)

/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















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[ccp4bb] Industrial crystallographer position in Lund, Sweden

[Derek Logan]

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 Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden


SARomics Biostructures is one of the fast-growing biotech companies in Lund. We 
strive to accelerate drug discovery through structural insight. Our 
international team of over 25 researchers covers the following fields of 
expertise: protein engineering, protein production and characterization, 
biophysical screening, protein NMR analysis, protein X-ray crystallography, 
fragment screening, and computational chemistry. SARomics has built a global 
reputation for its structural biology platform and structure-based drug design 
skills and is currently supporting mainly international clients in pursuing 
their drug discovery objectives. In parallel, the company is pursuing several 
internal drug discovery projects to discover leads for new medicines.

We seek highly motivated and skilled X-ray crystallography scientists to expand 
and strengthen our teams, which work on protein production and crystallization. 
The ideal candidate will be self-driven, resourceful, organized, focused, 
service-minded, and enjoy working in a dynamic, fast-paced team environment. 
The candidate should have a strong desire to learn new techniques and 
incorporate new methodologies into their work, and carry out innovative and 
high-quality research to answer challenging questions in structural biology.

Successful candidates’ requirement:

  *   Ph.D. in structural biology or related fields
  *   Work closely with an experienced team of interdisciplinary researchers 
and have regular opportunities to present findings to the project team, senior 
management, and clients
  *   Have excellent analytical, organizational, and communication skills - 
fluency in English (spoken and written) is expected
  *   Ability and desire to work in a fast-paced, dynamic environment to ensure 
timely progress in customers' projects
  *   Analyze, document, and report experimental data
  *   Legally authorized to work in Sweden

Required knowledge, skills, and abilities:

  *   Experience in protein crystallization using a wide variety of proteins
  *   Experience in all steps of structure determination (including data 
collection and refinement)
  *   An ideal candidate will also have had experience with structure-based 
design and drug discovery projects

The successful candidate will get the opportunity:

  *   to join an energetic and enthusiastic international team with a focus on 
scientific excellence and teamwork
  *   to evolve in a highly multidisciplinary environment and thus develop new 
competencies outside their core expertise
  *   to accelerate discovery through structural insight

Please explore our website to find out what it is like to work at SARomics 
Biostructures: http://www.saromics.com/
For specific questions regarding the position, please call Nadia Rose or Martin 
Welin (+46 46 26 10 474).

If you are interested in a career with us, please forward a CV/resume and a 
cover letter to i...@saromics.com and label your message with the subject “SBX 
Career”. We will interview candidates continuously and would therefore like to 
receive your application as soon as possible. The application should be in 
English.
















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Re: [ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

Hi Christian,

Thanks for pointing out that option. I will definitely try it out. Perhaps my 
tutorial can be adapted to this way of making the models.

/Derek

On 16 Oct 2020, at 10:26, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:

HI Derek,
I don't know which options you 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 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 the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


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[ccp4bb] MrBUMP in CCP4I2

[Derek Logan]

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 the students solving 
the thaumatin structure using two different search models with higher and lower 
sequence identity, which involves specifying them individually. The advantage 
of using MrBUMP is that the students don't have to do a separate step with 
Chainsaw or Sculptor. What's more, we do one run with and one run without 
automated model building and refinement for each model to compare the final 
results. CCP4I2 doesn't seem to offer any of these options.

Of course I can run the tutorial using CCP4I but I was trying to "modernise" it 
a bit.

Any advice is welcome
Derek


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

[Derek Logan]

Hi Jon & Robbie,

Yes, that did the trick. I must have missed the whole discussion on how 
treatment of carbohydrates has changed since I refined this glycosylated 
protein. Strangely, Refmac still complains that OXT is missing from every 
residue in the structure, but at least it doesn't bomb out now and the 
refinement runs to completion.

Thanks for your rapid answers!
Derek

On 28 Nov 2018, at 17:29, Jon Agirre 
mailto:jon.agi...@york.ac.uk>> wrote:

Dear Derek,

does the PDB in question have MODRES records in the header? These re-define the 
names of NAG, etc to something else that may not be handled by today's monomer 
library, as the different anomeric forms are now tied to the three letter code 
you are using (NAG -> beta-D-GlcNAc). I think it might just work if you get rid 
of all MODRES records in your PDB?

Let me know if that does the trick!

Best regards,
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. Essentially refmac seems to think that every residue is a 
terminal one, as it complains that OXT is missing 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
Associate Professor, Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se<http://www.cmps.lu.se/>

 --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name mon_lib

 _lib_version  5.51

 _lib_update   11/07/18

  --

  --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name ?

 _lib_version  ?

 _lib_update   ?

  --

  WARNING: duplicated name of monomer 935

   Last entry will be used.

  NUMBER OF MONOMERS IN THE LIBRARY  : 24613

with complete description: 24613

  NUMBER OF MODIFICATIONS:71

  NUMBER OF LINKS:77

  I am reading libraries. Please wait.

  - energy parameters

  - monomer"s description (links & mod )

  Number of atoms:3107

  Number of residues : 620

  Number of chains   :   8

  I am reading library. Please wait.

mon_lib.cif

  WARNING : residue: ASP 1  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: THR 2  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: PRO 3  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: ALA 4  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: ASN 5  chain:AAA

atom: "OXT " is absent in coord_file

[and so on for every residue in the structure]

[snip]

WARNING : residue: NAG-b-D 604 chain:BaB - is not in the library

  WARNING : monomer looks like 5AX ;

  WARNING : the program will try to use 5AX

  WARNING : residue: NAG-b-D   604  chain:BaB  - rename

   "NAG-b-D " --> "5AX "

[etc.]

For comparison, here is the output from 2009:

--

  ---  LIBRARY OF MONOMERS   ---

 _lib_name mon_lib

 _lib_version  4.16

 _lib_update   29/09/08

  --

  --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name ?

 _lib_version  ?

 _lib_update   ?

  --

  NUMBER OF MONOMERS IN THE LIBRARY  :  2446

with complete description:   465

  NUMBER OF MODIFICATIONS:50

  NUMBER OF LINKS:65

  I am reading libraries. Please wait.

  - energy parameters

  - monomer"s description (links & mod )

 [CRYST1 line removed]

  Number of atoms:3107

  Number of residues : 620

  Number of chains   :   8

  I am reading library. Please wait.

mon_lib.cif

  WARNING : residue: NAG   602  chain:Aa

atom: "O1  " is absent in coord_file

  WARNING : residue: NAG   604  chain:Ba

atom: "O1  " is absent in coord_file

  WARNING : residue: LEU   439  chain:CC

atom: "OXT " is absent in coord_file

and very little else
















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[ccp4bb] Refmac5 crashes with coordinates last refined in 2009

[Derek Logan]

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 refmac seems to think that every residue is a 
terminal one, as it complains that OXT is missing 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
Associate Professor, Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se<http://www.cmps.lu.se>

 --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name mon_lib

 _lib_version  5.51

 _lib_update   11/07/18

  --

  --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name ?

 _lib_version  ?

 _lib_update   ?

  --

  WARNING: duplicated name of monomer 935

   Last entry will be used.

  NUMBER OF MONOMERS IN THE LIBRARY  : 24613

with complete description: 24613

  NUMBER OF MODIFICATIONS:71

  NUMBER OF LINKS:77

  I am reading libraries. Please wait.

  - energy parameters

  - monomer"s description (links & mod )

  Number of atoms:3107

  Number of residues : 620

  Number of chains   :   8

  I am reading library. Please wait.

mon_lib.cif

  WARNING : residue: ASP 1  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: THR 2  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: PRO 3  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: ALA 4  chain:AAA

atom: "OXT " is absent in coord_file

  WARNING : residue: ASN 5  chain:AAA

atom: "OXT " is absent in coord_file

[and so on for every residue in the structure]

[snip]

WARNING : residue: NAG-b-D 604 chain:BaB - is not in the library

  WARNING : monomer looks like 5AX ;

  WARNING : the program will try to use 5AX

  WARNING : residue: NAG-b-D   604  chain:BaB  - rename

   "NAG-b-D " --> "5AX "

[etc.]

For comparison, here is the output from 2009:

--

  ---  LIBRARY OF MONOMERS   ---

 _lib_name mon_lib

 _lib_version  4.16

 _lib_update   29/09/08

  --

  --

  ---  LIBRARY OF MONOMERS   ---

 _lib_name ?

 _lib_version  ?

 _lib_update   ?

  --

  NUMBER OF MONOMERS IN THE LIBRARY  :  2446

with complete description:   465

  NUMBER OF MODIFICATIONS:50

  NUMBER OF LINKS:65

  I am reading libraries. Please wait.

  - energy parameters

  - monomer"s description (links & mod )

 [CRYST1 line removed]

  Number of atoms:3107

  Number of residues : 620

  Number of chains   :   8

  I am reading library. Please wait.

mon_lib.cif

  WARNING : residue: NAG   602  chain:Aa

atom: "O1  " is absent in coord_file

  WARNING : residue: NAG   604  chain:Ba

atom: "O1  " is absent in coord_file

  WARNING : residue: LEU   439  chain:CC

atom: "OXT " is absent in coord_file

and very little else
















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Re: [ccp4bb] Unrecognised argument problem in AMPLE

[Derek Logan]

Hi Jens,

Yes, I'm running it from CCP4i. I should have made that explicit in my first 
e-mail. I somehow never quite graduated to CCP4i2. I suspected a disconnect 
between the GUI and the code, so it's good to know that you're on top of it. I 
look forward to the update!

Best regards
Derek

> On 18 Jan 2018, at 11:11, Thomas, Jens <jens.tho...@liverpool.ac.uk> wrote:
> 
> Dear Derek,
> 
> Sorry to hear that you've had problems running AMPLE. We've made a number of 
> updates recently and it looks like you've encountered a problem with the gui 
> and the code becoming 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 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Derek Logan 
> <derek.lo...@biochemistry.lu.se>
> Sent: 18 January 2018 08:43:34
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [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 offending one. 
> Has anyone run into this before? It also fails if I choose to use ARP/wARP, 
> saying that it doesn't understand the argument -use_arpwarp True... My CCP4 
> installation is fully up-to-date.
> 
> Thanks
> Derek

[ccp4bb] Unrecognised argument problem in AMPLE

[Derek Logan]

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 offending one. 
Has anyone run into this before? It also fails if I choose to use ARP/wARP, 
saying that it doesn't understand the argument -use_arpwarp True... My CCP4 
installation is fully up-to-date.

Thanks
Derek

[ccp4bb] Problems with QT graphs in Aimless log files

[Derek Logan]

Hi,

I'm running CCP4 version 7.0.047 on a number of Linux PCs with OpenSUSE Linux 
as part of a course. I'm having problems with visualising Aimless log files, at 
least the graphical part. The graphs simply don't show up in the QT visualiser. 
Scala doesn't suffer from the same problem. Has anyone else run into this? I 
had a similar problem with Phaser output 4 years ago on the Windows systems 
that we used then, and that was due to the lack of a User: line in the Phaser 
output that meant that the log file couldn't be parsed properly. Could this be 
a related problem? I don't have this issue on my Mac.

Thanks
Derek Logan

[ccp4bb] Crystallographer position at SARomics Biostructures

[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

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

[Derek Logan]

Hi Nick, Pavel and Herman,

Thanks for the lightning-fast tip about not using an altconf label for the 
common part of the molecule. That was the solution. So obvious when you think 
about it... My colleague Esko Oksanen also pointed out offline that I need to 
include the last atom before the phenyl ring with two conformations, otherwise 
the torsion angle wouldn't be properly defined. Indeed, without including this 
atom it blew up when idealising geometry in Coot, but with that minor 
modification it behaved just fine in both phenix.refine and Refmac.

@Pavel, thanks but it wasn't a visualisation glitch, as the rings were clearly 
displaced from each other. (BTW my message got bounced from phenixbb because of 
the screen dump I included).

/Derek


On 27 Oct 2017, at 13:47, Nick Pearce 
<n.m.pea...@uu.nl<mailto:n.m.pea...@uu.nl>> wrote:

Conformer A atoms don’t “see” conformer B atoms so as far as the program is 
concerned the B conformer only has the last ring.
You should set all confA atoms not in the last ring to blank conformers.

So:
last ring - A +B conformers
rest of ligand - no conformer

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral 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 largish 
small molecule ligand. It has two conformations that differ only in the 
orientation of a terminal aromatic ring, i.e. variation in the last torsion 
angle. I previously refined it as two independent conformations for the whole 
molecule, but that showed too much deviation between the conformations in the 
region that is "identical", i.e. that can be modelled just as nicely with a 
single conformation. With Occam's razor I split the molecule at the last 
torsion angle. Conformation A is the whole molecule; conformation B is just the 
last ring. Both have the same residue number, just different altloc labels. 
However when I refine this using phenix.refine, the B conformation refines as 
if it were not attached to the A conformation (see the attached screen dump). I 
tried it using Refmac and the two conformations separated even more. Clearly 
this didn't work as I was expecting. What am I doing wrong? Is it even possible 
to do it this way?

/Derek

Re: [ccp4bb] MrBUMP error

[Derek Logan]

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/python2.7/locale.py

and comment out lines 576-579, i.e.

#if locale and type(locale) is not type(""):
## convert to string
#locale = normalize(_build_localename(locale))
#return _setlocale(category, locale)

 I don't know if this is the most elegant solution, but it works and it doesn't 
seem to break anything else.

/Derek

On 5 Sep 2017, at 13:17, Nishant Varshney 
> wrote:

Dear Crystallographer,

I will be grateful if you help me with what may be a simple problem. While 
trying MrBUMP with my mtz file , I am currently getting the following error. 
Similar error I am getting while trying AMPLE as well.

"CCP4I VERSION CCP4Interface 7.0.044
#CCP4I SCRIPT LOG mrbump
#CCP4I DATE 01 Sep 2017  15:58:19
#CCP4I USER apple
#CCP4I PROJECT Josephin
#CCP4I JOB_ID 45
#CCP4I SCRATCH /tmp/apple
#CCP4I HOSTNAME Apples-iMac.local
#CCP4I PID 933

http_proxy not specified in environemnt
***
* Information from CCP4Interface script
***
The program run with command: /Applications/ccp4-7.0/bin/mrbump HKLIN 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1.mtz SEQIN 
/Users/apple/Documents/Nishant/Josephin_data/Phenix/Q15040.fasta HKLOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.mtz
 XYZOUT 
/Users/apple/Documents/Nishant/Josephin_data/ccp4/XDS_ASCII_scaled1_mrbump_soln1.pdb
 KEYIN /tmp/apple/Josephin_45_1_com.tmp
has failed with error message
Traceback (most recent call last):
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code
exec code in run_globals
  File "/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in 
import MRBUMP_master
  File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in 
import Matches
  File "/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", 
line 29, in 
import Write_MR_results
  File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in 
import printTable
  File "/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 
5, in 
locale.setlocale(locale.LC_NUMERIC, "")
  File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale
return _setlocale(category, locale)
locale.Error: unsupported locale setting
***


#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 162, in _run_module_as_main "__main__", fname, loader, pkg_name)   
File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py",
 line 72, in _run_code exec code in run_globals   File 
"/Applications/ccp4-7.0/lib/py2/mrbump/__main__.py", line 85, in  
import MRBUMP_master   File 
"/Applications/ccp4-7.0/share/mrbump/include/initialisation/MRBUMP_master.py", 
line 17, in  import MatchesFile 
"/Applications/ccp4-7.0/share/mrbump/include/structures/Matches.py", line 29, 
in  import Write_MR_results   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/Write_MR_results.py", line 
20, in  import printTable   File 
"/Applications/ccp4-7.0/share/mrbump/include/output/printTable.py", line 5, in 
 locale.setlocale(locale.LC_NUMERIC, "")   File 
"/Applications/ccp4-7.0/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
 line 579, in setlocale return _setlocale(category, locale) locale.Error: 
unsupported locale setting"
#CCP4I TERMINATION TIME 01 Sep 2017  15:58:20
#CCP4I TERMINATION OUTPUT_FILES   
/Users/apple/Documents/Nishant/Josephin_data/ccp4/search_45
#CCP4I MESSAGE Task failed


Looking forward for your help

Regards
Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690
<45_mrbump.log>

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

[Derek Logan]

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, Paul Emsley 
> wrote:


Hi Derek,

I have attached a script.  Drop it in your ~/.coot-preferences directory and 
restart your Coot. Should work (not tested).  If you want a specific mtz file, 
then you will have to use x-n-open via Calculate -> Scripting -> Scheme.

Paul.




xray-neutron.scm
Description: xray-neutron.scm

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

[Derek Logan]

Hi ccp4bb and phenixbb,

Is there a convenient way to open MTZ files in Coot that are the result of 
joint X-ray/neutron refinement in phenix.refine, but where phenix.refine was 
run in command-line mode? I would like achieve what is done in the Phenix GUI 
at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and 
Fo-Fc maps for both neutron and X-ray. At the moment I have to open each MTZ 
file four times in the Coot GUI, once for each type of map. Is there a script 
buried somewhere in the Phenix installation that can be modified?

/Derek

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>
Centre for Molecular Protein Science  bit.ly/2d0HxmS
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] Latest XQuartz upgrade breaks Coot

[Derek Logan]

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 /Library/Coot/bin. It seems 
from your experience that it doesn't affect the latest compiled versions from 
Bill. Regarding the contents of /opt/X11/lib, I have:

lrwxr-xr-x  1 root  wheel  26 Sep 27 17:19 /opt/X11/lib/libXt.6.dylib -> 
/opt/X11/lib/libXt.7.dylib
-rwxr-xr-x  1 root  wheel  698896 Sep 27 07:45 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x  1 501   wheel  13 Sep 27 10:43 /opt/X11/lib/libXt.dylib -> 
libXt.7.dylib
-rwxr-xr-x  1 root  wheel   71104 Sep 27 07:45 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x  1 501   wheel  15 Sep 27 10:43 /opt/X11/lib/libXtst.dylib -> 
libXtst.6.dylib

where the first line is the link I made myself. So libXt.6.dylib seems to have 
been removed in the latest release.

/Derek

On 28 Sep 2016, at 13:16, Logan Donaldson 
> wrote:

I’m running 10.12.1b2 but not the newest X11 yet.

The quick and dirty permanent way would be to use

install_name_tool -change /opt/X11/lib/libXt.6.dylib /opt/X11/lib/libXt.7.dylib 
coot-bin

I just installed coot-0.8.6.pkg from the Scott lab (for 10.11) and when I 
checked the binary, it already knew to look for libXt.7

LDMBP2015 [7:12am] /Library/Coot/bin
16 % otool -L 
coot-bin | grep libXt
/opt/X11/lib/libXt.7.dylib (compatibility version 8.0.0, current version 8.0.0)

19 % ls -l /opt/X11/lib/libXt*
-rwxr-xr-x  1 root   wheel  725856 May  5 04:33 /opt/X11/lib/libXt.6.dylib
-rwxr-xr-x  1 root   wheel  694640 May  5 04:33 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x  1 logan  wheel  13 May  5 13:56 /opt/X11/lib/libXt.dylib -> 
libXt.7.dylib
-rwxr-xr-x  1 root   wheel   71088 May  5 04:33 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x  1 logan  wheel  15 May  5 13:56 /opt/X11/lib/libXtst.dylib -> 
libXtst.6.dylib

-logan donaldson

[ccp4bb] Latest XQuartz upgrade breaks Coot

[Derek Logan]

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 solved this temporarily by soft-linking 
libXt.6.dylib to libXt.7.dylib. Has anyone else run into this and are there 
alternative solutions?

/Derek

[ccp4bb] Formulatrix NT8

[Derek Logan]

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 tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal
Lund University, Box 124, 221 00 Lund, Sweden

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

[Derek Logan]

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 David C Briggs PhD
http://about.me/david_briggs

On 1 Apr 2015 12:07, Keller, Jacob 
kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org wrote:
Can anyone index this? It's got mostly split spots and a strange diffuse 
scattering background

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org
***

[ccp4bb] Cross-validation when test set is miniscule

[Derek Logan]

Hi everyone,

Right now we have one of those very difficult Rfree situations where it's 
impossible to generate a single meaningful Rfree set. Since we're in a bit of a 
hurry with this structure it would be good if someone could point me in the 
right direction. We have crystals with 1542 non-H atoms in the asymmetric unit 
that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections 
in total. 5% of this is only about 100 reflections. Luckily the protein is only 
a single point mutation of a wild type that has been solved to much better 
resolution, so we know what it should look like and I simply want to 
investigate the effect of different levels of conservatism in the refinement, 
e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran 
restraints etc. However since the quality criterion for this is Rfree I'm not 
able to do this.

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

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal
Lund University, Box 124, 221 00 Lund, Sweden   www.saromics.com

[ccp4bb] Eleanor interview on Swedish radio

[Derek Logan]

Hi,

Swedish radio is currently doing a short series of programmes about 
crystallography and I just had the great pleasure of listening to a 73-minute 
(!)  interview with Eleanor D about Dorothy Hodgkin. It was very informative 
and complementary to the biography by Georgina Ferry. It seems a shame that we 
in Sweden should be the only ones to benefit from this, so here’s the link, for 
your listening pleasure:

http://sverigesradio.se/sida/avsnitt/460027?programid=412playaudio=5135276

It may only be available for 30 days, I’m not sure. Apart from a very brief 
introduction in Swedish 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 tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal
Lund University, Box 124, 221 00 Lund, Sweden   www.saromics.com

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

[Derek Logan]

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 it in a specific 
place. Anyway, I fixed it by making a symbolic link from /usr/X11R6 to 
/opt/X11R6 and likewise for /usr/X11:

lrwxr-xr-x 1 root  wheel8 Oct 24 19:52 X11 - /opt/X11
lrwxr-xr-x 1 root  wheel8 Oct 24 19:55 X11R6 - /opt/X11

Otherwise 10.10 works fine for me.

Hope ths helps
Derek

On 29 Oct 2014, at 14:45, Sebastiano Pasqualato 
sebastiano.pasqual...@gmail.commailto:sebastiano.pasqual...@gmail.com wrote:


Hi folks,
sorry for the off-topic and slightly ‘demodée’ question, but, since I updated 
to Yosemite on my Mac, nedit does not work any more.
Here’s the error message:

Seba@host041:~ nedit
dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib
  Referenced from: /Applications/nedit/nedit
  Reason: image not found
Trace/BPT trap: 5
Seba@host041:~

Anybody knows if there is a fix for that?
Thanks in advance,
S



--
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990
web http://is.gd/IEO_XtalUnit

[ccp4bb] PhD position in structural biology at Lund University

[Derek Logan]

Doctoral student in molecular biophysics
Type of employment: Limit of tenure, Four years 
Extent: 100 % 
Location: Department of Chemistry, Division of Biochemistry and Structural 
Biology, Lund 
First day of employment: 2014-10-01 

Research assignments
The PhD student will work with structural studies of protein-ligand 
interactions, using the carbohydrate-binding protein galectin-3 as a model 
system. The doctoral work is part of a larger project involving seven research 
groups at LU that aims at a detailed dissection of the roles of enthalpy and 
entropy role in protein-ligand interactions. The student will determine the 
structures of a large number of complexes of galectin-3 with novel synthetic 
ligand using X-ray crystallography at ultra-high resolution, as well as a 
smaller number of neutron crystal structures of selected complex. The work will 
include the purification of proteins, production of crystals (of normal size 
for X-ray diffraction and very large crystals for neutron studies), X-ray and 
neutron data collection and processing and modelling. The project will involve 
interaction with research groups engaged in organic synthesis, biophysical 
characterisation, in vitro and cell-based assays and quantum mechanics 
calculations.

Eligibility requirements
Students with basic eligibility for third-cycle studies are those who have 
completed a second-cycle degree, have completed courses of at least 240 
credits, of which at least 60 credits are from second-cycle courses, or have 
acquired largely equivalent knowledge in some other way, in Sweden or abroad. 
Special eligibility requirements comprise knowledge from first-cycle studies or 
the equivalent, but can also refer to special professional experience. 
Additionally, sufficient knowledge of the subject area is required for 
third-cycle studies. Students meeting special eligibility requirements are 
those who have at least 60 higher education credits within the same subject 
area as the third-cycle studies, of which in-depth work of at least 30 higher 
education credits of relevance to the subject area, a Swedish medical degree or 
Swedish certification as a doctor.

Special requirements for this position: The candidate must have Bachelor's 
degree in an appropriate subject (preferably Chemistry) and will ideally have 
previous experience in structural biology, both theoretical and practical. The 
candidate should also be proficient in physical chemistry, especially 
thermodynamics. Ability to work as part of a team that spans multiple 
disciplines, but at the same time to take responsibility for their own work and 
drive it forward is fundamental, as the research group is involved in a variety 
of other projects.

Document to include with the application: A summary (1/2-1 page) motivating why 
you wish to perform a PhD education in molecular biophysics at Lund University, 
and how the present research project matches your own research interests and 
scientific background.

Doctoral candidates may be required to work with educational tasks and 
administration in addition to research, up to a level of approximately 20%.

See here for more details and instructions on how to apply:

http://www.lu.se/lediga-anstallningar-available-jobs?x=0Dnr=615182Type=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

Re: [ccp4bb] 2 ligands/monomer

[Derek Logan]

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 second and third sites, but 
not as a substrate. It cannot bind to sites (c) and (s) at the same time 
although it could potentially bind to sites (s) and (a) simultaneously. Here is 
a review that you might find useful:

http://www.ncbi.nlm.nih.gov/pubmed/22050358

Best wishes
Derek

On 4 Mar 2014, at 04:48, Wei Shi wei.shi...@gmail.com wrote:

 Dear all,
 Does anyone happen to know examples of 2 ligands bind to a single protein / 
 each monomer protein in 2 different ligand binding pockets? 
 I know the following example:
 (1). phosphofructokinase, which binds ATP as both a ligand and a feedback 
 inhibitor in different sites 
 (2).  2 cAMP bound to each E. coli CAP monomer in the crystal structure. 
 
 Does any of you know other examples? Thank you so much!
 
 Best,
 Wei 

Re: [ccp4bb] What really happens in XDSCONV?

[Derek Logan]

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 much room 
 for mistakes.

Exactly!

 I beg to disagree, and this was the point of my question. The output of 
 XDSCONV literally says that 190093 reflections are read, and [of those, my 
 interpretation] 44047 are accepted. I may be a pedant but I can't read that 
 output in any other way. To me it looks like it is reading only the 
 reflections that already fall into the asymmetric unit and is ignoring all 
 the others. So if XDSCONV is really doing what it is supposed to, I would 
 suggest rephrasing that output line.
 
 good point about the rephrasing. I'll see to making the wording consistent 
 between XDSCONV and XDS.

Thanks for that.

 But irrespective of the wording, it does take all observations into account 
 when calculating the intensity (and amplitude) of the unique reflections (as 
 it should - ignoring reflections would not make sense, and would produce 
 significantly worse data).

Great, this was just the reassurance I was looking for.

 However, it does so not by calculating the geometric mean (which you seem to 
 assume), but by calculating the weighted mean. Weighting is done with the 
 variances, and here it also does not differ from (c)truncate or other 
 programs.

Sorry, that was a typo born of thinking I could quote the manual from memory.

 But yes, pedantry aside, I will start using pointless in my csh pipelines.
 
 please report back whether that changes (or even improves) your results! It 
 is always very good when people compare programs in a meaningful way, but 
 from my own experience I can say that meaningful comparisons are sometimes 
 not entirely straightforward to get right. (for the German-speaking: wer 
 misst, misst Mist!)

Probably I will still be in too much of a hurry each time to make a meaningful 
and thorough comparison, but if time allows I will compare XDSCONV with 
pointless/scala.

/Derek

[ccp4bb] What really happens in XDSCONV?

[Derek Logan]

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 to believe that 
XSCALE was always necessary, and I always use it in my workflow even if there 
is only one dataset (after all, there's nothing to lose), but my Ph.D. students 
pointed out to me that XDSCONV could take output directly from CORRECT, and 
they often do it this way. The XDS wiki and XDSCONV docs seems to confirm this: 
using MERGE=TRUE in XDSCONV should output the geometrical mean of the 
observations. However I am worried by what the XDSCONV output says. For today's 
example CORRECT gives me this:

NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  190093
NUMBER OF REJECTED MISFITS3842
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 34
NUMBER OF ACCEPTED OBSERVATIONS 186217
NUMBER OF UNIQUE ACCEPTED REFLECTIONS44059

XDSCONV says the following:

FRIEDEL'S_LAW=TRUE
MERGE=TRUE
NUMBER OF REFLECTION RECORDS ON INPUT FILE  190093
NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)   19
NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE   44047

To my literal mind this says it is throwing away most of the observations. Now 
if I merge the reflections in XSCALE first it says this:

FRIEDEL'S_LAW=TRUE
MERGE=TRUE
NUMBER OF REFLECTION RECORDS ON INPUT FILE   44046
NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)0
NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE   44046

which makes more sense. If I compare the first few reflections of the output 
file with structure factor amplitudes from XDSCONV for each scenario they are 
different, but I believe that is because XSCALE has put the intensities on an 
absolute scale and CORRECT has not.

Basically all I want to know is that the output from XDSCONV is misleadingly 
worded, i.e. that even if it appears to say that only the asymmetric unit has 
been accepted, actually all observations 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 mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Science   
www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] What really happens in XDSCONV?

[Derek Logan]

Hi Tim,

 I would actually recommend using pointless (or xprep) instead of
 xdsconv. It is much easier to use and maybe even less error prone.

I take the point about pointless but XPREP is commercial software sold by 
Bruker and costs €700 (as I remember), so is not really an option for everyone.

 All your quotes from the output are perfectly consistent. The first
 table tells you there are 190093 unmerged reflections in total, but
 only 44059 unique reflections. Hence if you ask xdsconv to merge the
 output (MERGE=TRUE), it will do so and only write 44047 (a few less
 than 44059 because it rejects those 19 unmerged reflections with
 I-3sigma).

I beg to disagree, and this was the point of my question. The output of XDSCONV 
literally says that 190093 reflections are read, and [of those, my 
interpretation] 44047 are accepted. I may be a pedant but I can't read that 
output in any other way. To me it looks like it is reading only the reflections 
that already fall into the asymmetric unit and is ignoring all the others. So 
if XDSCONV is really doing what it is supposed to, I would suggest rephrasing 
that output line.

 The documentation tells you:
 MERGE=TRUE means that the weighted mean of symmetry equivalent
 reflection intensities appearing in the input file will be determined
 and used in the output file.

Yes, I paraphrased this in my original mail. I like to believe that the manual 
describes what the program is doing, but the output isn't consistent with this 
in my view.

 xscale does not scale data in a crystallographic sense since scaling
 is already done in the CORRECT step of XDS. It put the data on a
 common scale (in a sophisticated manner), i.e. if you only have one
 data set there is no need to run xscale except for the thinner shells
 for the statistics table compared to CORRECT.

No need indeed, except that including XSCALE doesn't leave me sleepless about 
the data having been merged. And maybe correction for radiation damage when you 
have 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 constant angst about losing observations because
 I don't understand what goes in in the conversion steps to get to
 CCP4 format. I used to believe that XSCALE was always necessary,
 and I always use it in my workflow even if there is only one
 dataset (after all, there's nothing to lose), but my Ph.D. students
 pointed out to me that XDSCONV could take output directly from
 CORRECT, and they often do it this way. The XDS wiki and XDSCONV
 docs seems to confirm this: using MERGE=TRUE in XDSCONV should
 output the geometrical mean of the observations. However I am
 worried by what the XDSCONV output says. For today's example
 CORRECT gives me this:
 
 NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES  190093 NUMBER
 OF REJECTED MISFITS3842 NUMBER OF
 SYSTEMATIC ABSENT REFLECTIONS 34 NUMBER OF ACCEPTED
 OBSERVATIONS 186217 NUMBER OF UNIQUE ACCEPTED
 REFLECTIONS44059
 
 XDSCONV says the following:
 
 FRIEDEL'S_LAW=TRUE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT
 FILE  190093 NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)
 19 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE   44047
 
 To my literal mind this says it is throwing away most of the
 observations. Now if I merge the reflections in XSCALE first it
 says this:
 
 FRIEDEL'S_LAW=TRUE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT
 FILE   44046 NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)
 0 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE   44046
 
 which makes more sense. If I compare the first few reflections of
 the output file with structure factor amplitudes from XDSCONV for
 each scenario they are different, but I believe that is because
 XSCALE has put the intensities on an absolute scale and CORRECT has
 not.
 
 Basically all I want to know is that the output from XDSCONV is
 misleadingly worded, i.e. that even if it appears to say that only
 the asymmetric unit has been accepted, actually all observations
 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 mob: +46 76
 8585 707 Dept. of Biochemistry and Structural Biology
 www.cmps.lu.sehttp://www.cmps.lu.se Centre for Molecular Protein
 Science
 www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307 Lund
 University, Box 124, 221 00 Lund, Sweden
 
 
 
 
 
 
 
 - -- 
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12

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

[Derek Logan]

Hi,

David Waterman and Andrey Lebedev sorted out my problem with Phaser log file 
output in QtRView on Windows. 

It turns out that Phaser on Windows fails to write a User: line just under 
the program banner in the log. This line is necessary for proper processing of 
the log file. You can correct the broken log by adding a line like this:

#
#
#
### CCP4 PROGRAM SUITE: Phaser  
2.5.5 ###
#
User: fcx32934
Run time: Thu Dec 05 13:28:16 2013

David has promised that the developers will release 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 derek.lo...@biochemistry.lu.se wrote:

 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 version of Phaser using the 
 Windows CCP4I and the graphs are visible. This suggests it's not a problem 
 with the GUI but with the content of the log file generated by the Windows 
 Phaser. Any ideas?
 
 Thanks
 Derek

[ccp4bb] Phaser output in QtRView under Windows XP

[Derek Logan]

Hi,

I need (reluctantly!) to install CCP4 on 20 fairly ancient Windows XP machines 
for a course. I have installed CCP4 on a central server with network-mounted 
drive and applied all the updates. CCP4 is then runnable on the individual 
computers. However when I run a Phaser job the output in QtRView ouptut does 
not look the same as it does when I run the same job on my Mac. All the graphs 
are missing and the only sections displayed are Input Files and Output 
Files. I don't have the same problem for Refmac, where the graphs display 
correctly. I also tested 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

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Science   
www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

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

[Derek Logan]

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 version of Phaser using the 
Windows CCP4I and the graphs are visible. This suggests it's not a problem with 
the GUI but with the content of the log file generated by the Windows Phaser. 
Any ideas?

Thanks
Derek

Re: [ccp4bb] largest protein crystal ever grown?

[Derek Logan]

Hi Felix,

What was the mosaicity of this crystal? The absorption correction must have 
been challenging too...

Derek

On 25 Oct 2013, at 13:23, Felix Frolow 
mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il wrote:

Well if we start recalling rumours, I have heard that in  UC San Diego in the  
laboratory of  George Feher there was (is) a tetragonal hen egg white  lysozyme 
crystal
which weighted between 0.5 - 1.0 kg.
It grew suspend on a mountain boots shoelace  of the read colour.
I have never visited George laboratory, but maybe among the society there are 
some who can shed some light on that….
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Oct 25, 2013, at 12:18 , Boaz Shaanan 
bshaa...@bgu.ac.ilmailto:bshaa...@bgu.ac.il wrote:

Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing 
room (by now tho old one I guess), is that the one that was sitting in the 
largest part of the Pasteur pipette? I recall this one and I keep telling my 
students about it when they ask about crystal size limits.
Cheers, Boaz



 הודעה מקורית 
מאת: simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk
תאריך:
אל: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
נושא: Re: [ccp4bb] largest protein crystal ever grown?


Hi Derek,

That brings back memories.  I am pretty certain that is the myoglobin crystal 
that was already on Benno's shelf at Brookhaven when I went there in 1980 to 
collect my oxymyoglobin neutron data.  It would the metmyoglobin crystal Benno 
got the early neutron data from.  He just kept it on the shelf because there 
was, of course, no degradation in the beam and a crystal is a pretty stable way 
to store a protein.  Whenever he wanted more data he took it off the shelf and 
put it back on the beamline.  If Benno is reading this bulletin board I am sure 
he could tell us more.

Simon

Simon E.V. Phillips
Director, Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email: susan.jo...@rc-harwell.ac.ukmailto:susan.jo...@rc-harwell.ac.uk
Direct email: 
simon.phill...@rc-harwell.ac.ukmailto:simon.phill...@rc-harwell.ac.uk
Tel:   +44 (0)1235 567701 (direct)
   +44 (0)1235 567700 (sec)
   +44 (0)7884 436011 (mobile)
www:   www.rc-harwell.ac.ukhttp://www.rc-harwell.ac.uk/

-Original Message-
From: 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 exhibition-quality glass dome, was a crystal 
of myoglobin some 50 mm**3, if I remember correctly. I was told it had been 
made by Benno Schoenborn some decades earlier and had been exposed to most of 
the neutron sources in the world (radiation damage - forget about it!) Paul 
Langan or Zoë Fisher can correct me if I've exaggerated the size or age.

Anyway, as I already lost the record several times over for having seen the 
biggest protein crystal ever, I can share with you the surprise and delight of 
having to centre the crystals using a telescope mounted on a tripod on the 
other side of the room. Apparently the magnification on the microscope on the 
diffractometer (visible in this photo, and maybe the giant crystal too? 
http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363secret=291f519124)
 was too high, so any neutron-size crystals would filled the whole field of 
view even if they were not well-centered.

FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons 
even after a 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.sehttp://www.cmps.lu.se/
Centre for Molecular Protein Science   
www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

On 24 Oct 2013, at 18:35, Victor Lamzin 
vic...@embl-hamburg.demailto:vic...@embl-hamburg.de wrote:

 Also following on from John's comment - back to the times of my PhD I was 
 repeatedly growing crystals of bacterial formate dehydrogenase (80 kDa) of a 
 size about 7x1.5x1 mm. I thought that was quite normal and did not even think 
 of making a photo of 'just a protein crystal'.

 Victor
This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use

Re: [ccp4bb] largest protein crystal ever grown?

[Derek Logan]

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 
of myoglobin some 50 mm**3, if I remember correctly. I was told it had been 
made by Benno Schoenborn some decades earlier and had been exposed to most of 
the neutron sources in the world (radiation damage - forget about it!) Paul 
Langan or Zoë Fisher can correct me if I've exaggerated the size or age.

Anyway, as I already lost the record several times over for having seen the 
biggest protein crystal ever, I can share with you the surprise and delight of 
having to centre the crystals using a telescope mounted on a tripod on the 
other side of the room. Apparently the magnification on the microscope on the 
diffractometer (visible in this photo, and maybe the giant crystal too? 
http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363secret=291f519124)
 was too high, so any neutron-size crystals would filled the whole field of 
view even if they were not well-centered.

FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons 
even after a 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.se
Centre for Molecular Protein Science   www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

On 24 Oct 2013, at 18:35, Victor Lamzin vic...@embl-hamburg.de wrote:

 Also following on from John's comment - back to the times of my PhD I was 
 repeatedly growing crystals of bacterial formate dehydrogenase (80 kDa) of a 
 size about 7x1.5x1 mm. I thought that was quite normal and did not even think 
 of making a photo of 'just a protein crystal'.
 
 Victor

[ccp4bb] MAX IV Life Science Director position

[Derek Logan]

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 tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Science   
www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] MAX IV Life Science Director position

[Derek Logan]

Thanks Tim! But seriously, MAX IV will, as well as being a synchrotron, have a 
Short Pulse Facility at the end of its linac:

http://www.maxlab.lu.se/femtomax

By world's brightest light source of course I loaned a management slogan, but 
MAX IV will be a 3 GeV facility with emittance around 0.25 nmrad, which is a 
factor of 4 better than PETRA-III and will, at least as long as records tend to 
hold (i.e. not long), have the best specs in the world:

http://www.maxlab.lu.se/node/206

/Derek

On 3 Jun 2013, at 17:25, Tim Gruene t...@shelx.uni-ac.gwdg.de
 wrote:

 -BEGIN PGP SIGNED 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...@biochemistry.lu.se
 wrote:
 
 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 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 Protein Science 
 www.maxlab.lu.se/node/307 Lund University, Box 124, 221 00 Lund, 
 Sweden
 
 
 
 
 
 
 
 
 
 - -- 
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
 
 iD8DBQFRrLVvUxlJ7aRr7hoRAueEAJ4hMgXQ1RPQ/IhCiCHTEug1ofKDKQCg6X76
 eicKXxWNf20+O5eX5R4xOYM=
 =AmlU
 -END PGP SIGNATURE-

Re: [ccp4bb] Coot's hidden talents!

[Derek Logan]

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

On 11 Jan 2013, at 13:08, Mark J van Raaij mjvanra...@cnb.csic.es wrote:

 if you zoom in 10exp9-10exp10 times (lots of cmd-+ in macosx), you can see 
 the amino acids.
 
 tried to check the accuracy; however, I couldn't find the mtz file to display 
 the density...does this journal not enforce depositing the data?
 
 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 On 11 Jan 2013, at 11:47, Harry Powell wrote:
 
 Hi
 
 Just noticed this - 
 
  http://www.bbc.co.uk/news/uk-20978904
 
 do we know the artist? He has just moved to Cambridge...
 
 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
 Road, Cambridge, CB2 0QH
 Chairman of European Crystallographic Association SIG9 (Crystallographic 
 Computing) 
 
 
 
 
 
 

[ccp4bb] Ph.D. position at Lund University

[Derek Logan]

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 participation of ESS 
scientists. 

The PhD student will work on structural and theoretical studies of 
protein-ligand interactions, using the carbohydrate binding protein galectin-3 
as a model system. Structural studies will be conducted principally using 
neutron crystallography in combination with X-ray crystallography at very high 
resolution ( 0.9 Å). The work will include production of crystals of suitable 
size for neutron diffraction, data collection at various neutron sources around 
the world, processing and modelling. The theoretical studies will be conducted 
in Ulf Ryde's group at Theoretical Chemistry. We will develop methods to 
combine crystallographic refinement and quantum mechanical calculations. In 
addition, we perform molecular dynamic simulations and estimates of binding 
affinities using free-energy perturbation. The project is part of a larger 
network at Lund University including organic chemists, medical scientists and 
NMR experts, dedicated to a fundamental understanding of protein-ligand 
interactions in general and galectin inhibition in particular.

The candidate must have bachelor's degree in an appropriate subject (preferably 
chemistry), and should ideally have previous experience in structural biology, 
both theoretical and practical. The candidate should also have good knowledge 
of theoretical chemistry. Experience of quantum chemistry, statistical 
mechanics and simulations is an advantage.

The deadline for application is 31st January 2013.

For more information on the eligibility requirements, please see:

http://admin.lu.se/o.o.i.s?id=22598Dnr=511988Type=E

For further information on the project please contact: 
Derek Logan, Senior lecturer 
+46 46-2224584 
derek.lo...@biochemistry.lu.se

Ulf Ryde, Professor 
+46-2224502 
ulf.r...@teokem.lu.se

http://www.cmps.lu.se/
http://www.teokem.lu.se/
http://www.chem.lu.se/People/galectins_in_Lund/
http://www.esss.se

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

[Derek Logan]

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/pm_exteriornew.html

You can see that the lawn outside has been severely affected by the reality 
distortion field. Actually Apple seem to have moved away from the monolithic 
design in Fred's mail towards something greener (well with grass on the roof 
anyway...) and more compact. Check out another, even more elegant earlier 
design here:

http://www.maxlab.lu.se/maxlab/max4/images/maxiv_buildning_suggestions/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: +46 76 8585 707
Centre for Molecular Protein Science   www.cmps.lu.se
Lund University, Box 124, 221 00 Lund, Sweden  www.saromics.com

On 9 Jun 2011, at 17:49, Vellieux Frederic wrote:

 Sorry, a bit off topic. But in the news today (check google news for 
 example): Steve Jobs (Apple) has revealed his plans for the new Apple 
 campus (Apple headquarters) in Cupertino, California. Should look familiar 
 to macromolecular crystallographers.
 
 Fred.
 apple.jpg

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

[Derek Logan]

Hi Harry,

Apple, GCHQ, what's the difference?
http://petewarden.github.com/iPhoneTracker/

/Derek

P.S. Apple seem to have done a significantly better job of the car parking 
issue...

On 12 Jun 2011, at 21:17, Harry wrote:

 Hi
 
 Hmmm. I was actually struck by the similarity between Apple's new HQ and 
 GCHQ, the UK government's top-secret communications monitoring station -
 
 http://www.google.co.uk/searchq=gchqhl=enclient=safarirls=enbiw=1175bih=764prmd=ivnsmsource=lnmstbm=ischei=hA_1TYeHJYOw8gOC1NSXBwsa=Xoi=mode_linkct=modecd=2sqi=2ved=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,
 
 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/pm_exteriornew.html
 
 You can see that the lawn outside has been severely affected by the reality 
 distortion field. Actually Apple seem to have moved away from the monolithic 
 design in Fred's mail towards something greener (well with grass on the 
 roof anyway...) and more compact. Check out another, even more elegant 
 earlier design here:
 
 http://www.maxlab.lu.se/maxlab/max4/images/maxiv_buildning_suggestions/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: +46 76 8585 707
 Centre for Molecular Protein Science   www.cmps.lu.se
 Lund University, Box 124, 221 00 Lund, Sweden  www.saromics.com
 
 On 9 Jun 2011, at 17:49, Vellieux Frederic wrote:
 
 Sorry, a bit off topic. But in the news today (check google news for 
 example): Steve Jobs (Apple) has revealed his plans for the new Apple 
 campus (Apple headquarters) in Cupertino, California. Should look familiar 
 to macromolecular crystallographers.
 
 Fred.
 apple.jpg
 
 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
 Cambridge, CB2 0QH
 

Re: [ccp4bb] Dehydration treatments

[Derek Logan]

Hi,

Yes indeed, as Matt was kind enough to point out, we do have the HC1 installed 
at station I911-3 of the MAX-II ring and you are welcome to make a rapid access 
application. One advantage of MAX-lab might be that our wiggler beam is more 
merciful to the crystals at room temperature than 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 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
Lund University, Box 124, 221 00 Lund, Sweden  www.saromics.com




On May 2, 2011, at 8:11, Matthew BOWLER wrote:

 Dear Israel,
 as Martin pointed out we have a device here at the ESRF/EMBL, the 
 HC1b,  that produces a stream of air with a precisely controlled RH at 
 the sample position that we have used with some success to monitor the 
 effects dehydration has on diffraction quality.  The same device is also 
 available at Diamond, Max-Lab and, I believe, BESSY. The example you 
 describe is a classic example of the sort of system that will usually 
 benefit from controlled dehydration.  Depending on the size and 
 concentration of the LMW PEG you are using you have probably reduced the 
 RH surrounding your crystal by ~10%.  The best thing to do now is 
 repeat these experiments using the HC1b to really define the changes in 
 the lattice of your crystals and find the optimum dehydration conditions 
 for your crystals.  At the ESRF the device can be requested for any 
 experimental session (just click the check box on the A form) and I 
 presume that this will be similar at the other synchrotrons.
 
 As well as the reference describing the device we have recently 
 published a further description of typical experimental conditions and 
 some successful applications:
 
 http://dx.doi.org/10.1016/j.jsb.2011.03.002
 
 And the ESRF webpage is here:
 
 http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b
 
 Good luck!  Matt
 
 
 On 01/05/2011 19:32, Israel Sanchez wrote:
 Hi folks,
 
 
 I am currently impressed by the efficiency of dehydration treatments 
 over the diffraction capacity of our crystals in one particular 
 condition. Without any treatment the crystals seldom diffract to 
 20-30A but in our last synchrotron trip the very same crystals, after 
 been incubated with increasing concentration of low molecular weight 
 PEGs diffracted to 6A.
 
 I was wondering if anyone has studied these effects in a systematic 
 way. Does anyone on the ccp4bb knows  references or has any 
 experience/pseudo-religious believes that do not care to share with 
 the community about this particular topic?
 
 
 Thank you very much in advance
 
 
 -- 
 Israel Sanchez Fernandez PhD
 Ramakrishnan-lab
 MRC Laboratory of Molecular Biology,
 Hills Road, Cambridge, CB2 0QH, UK
 
 
 
 -- 
 Matthew Bowler
 Structural Biology Group
 European Synchrotron Radiation Facility
 B.P. 220, 6 rue Jules Horowitz
 F-38043 GRENOBLE CEDEX
 FRANCE
 ===
 Tel: +33 (0) 4.76.88.29.28
 Fax: +33 (0) 4.76.88.29.04
 
 http://go.esrf.eu/MX
 http://go.esrf.eu/Bowler
 ===

Re: [ccp4bb] AMP-PNP Hydrolysis

[Derek Logan]

Hi Steve,

Funnily enough I just read the following paper today, which describes exactly 
this phenomenon:

http://www.ncbi.nlm.nih.gov/pubmed/21093442

Is AMPPCP as sensitive to acid conditions? I would suspect not.

Best wishes
Derek
___
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 University, Box 124, 221 00 Lund, Sweden  
www.saromics.comhttp://www.saromics.com

On Feb 14, 2011, at 15:05, Young-Jin Cho wrote:

Hi Steve,

With my experience, it is (very) common to see AMPPNP is hydrolyzed to AMPPN 
(supposedly) with my protein.  Although the literature often reported AMPPNP as 
a stable ATP mimic, such a luck wasn't true with my case, maybe same as you.  
If you go to Sigma website where I purchased, it may say it is not stable in an 
acidic condition.  My mother liquor was in an acidic condition. So you'd better 
consider if you used it in an acidic condition, otherwise, your protein 
inherently has a strong power to hydrolyze it.  In addition to the pH, I often 
see it can go hydrolysis easily.  However, you can try more as you mentioned it 
may contain impurity. I just want to inform you that it is not surprising to 
see this hydrolysis.

Good luck~

Young-Jin


On Mon, Feb 14, 2011 at 8:30 AM, Soisson, Stephen M 
stephen_sois...@merck.commailto:stephen_sois...@merck.com wrote:

Hi there,

Was recently looking at a structure of an enzyme with AMP-PNP added to the 
crystallization mix, and all I see is density for ADP.  I was wondering if 
hydrolysis of AMP-PNP to ADP is relatively common - either as a result of 
extended time in crystallization or exposure of the resultant crystals to 
synchrotron radiation?

I know that there can be up to 10% contamination of ADP in the purchased 
material, so it could just be that we have selected that form in the crystal, 
or that there was endogenous ADP bound that failed to substitute.  Just curious 
if hydrolysis is a common observation.

Thanks in advance-

Steve

Stephen M. Soisson, Ph.D.
Structural Chemistry Site Lead, WP

Merck Research Laboratories
770 Sumneytown Pike, WP14-1101
West Point, PA  19486
Phone:  (215) 652-6185
Fax:(215) 652-9051
stephen_sois...@merck.commailto:stephen_sois...@merck.com


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please notify us immediately by reply e-mail and then delete it from
your system.

[ccp4bb] XDS Viewer

[Derek Logan]

Hi,

I very recently downloaded and installed the Mac OS X executable of  
the new XDS Viewer program to inspect diffraction images. I have moved  
the program to /Applications. It starts up fine, but when I try to  
load an image it complains:


Cannot open file! For image formats other than .cbf you need to  
install the 2cbf script. Please make sure you have added it to the  
executable path.


Now 2cbf is in /usr/local/bin, which is in my path. I use /bin/tcsh as  
shell. Is there some confusion between the shell used by XDS Viewer  
(if any) and my preferred 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: +46 46 222 4692
Molecular Biophysics  mob: +46 76 8585 707
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] XDS Viewer

[Derek Logan]

Hi Andrzej,

Thanks for the tip. It just seemed to me that since the package  
installed as a typical Mac OS X clickable program, then it was meant  
to run that way. Thanks also for info about adxv. I wasn't aware that  
there was a Mac executable for this program.


Kay, the image I was trying to read was a .mar2560 file frpm the  
mar555 flat panel detector, which I had previously processed using XDS.


Cheers
Derek

On Mar 6, 2009, week10, at 8:10, Andrzej Lyskowski wrote:


Hi,

 Once you have a 2cbf in /usr/local/bin and start XDS Viewer from a
terminal (/Applications/XDS-Viewer.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 executable of  
the
new XDS Viewer program to inspect diffraction images. I have moved  
the
program to /Applications. It starts up fine, but when I try to load  
an

image it complains:

Cannot open file! For image formats other than .cbf you need to
install the 2cbf script. Please make sure you have added it to the
executable path.

Now 2cbf is in /usr/local/bin, which is in my path. I use /bin/tcsh  
as
shell. Is there some confusion between the shell used by XDS Viewer  
(if
any) and my preferred 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: +46 46 222 4692

Molecular Biophysics mob: +46 76 8585 707

Centre for Molecular Protein Science

Lund University, Box 124, 221 00 Lund, Sweden




__
Derek Logan   tel: +46 46 222 1443
Associate Professor   fax: +46 46 222 4692
Molecular Biophysics  mob: +46 76 8585 707
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] Mac pro

[Derek Logan]

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 waiting for today's announcements of the i7 core  
MacPro's ? If not wait another 6 hours before deciding to buy  
something.


Jürgen

On 6 Jan 2009, at 06:27, Sheemei wrote:


Dear all,
	I am thinking of getting a apple Mac pro desktop computer. I was  
wondering does all crystallography programs run on it? I think  
there are Mac OSX version of CCP4, CNS, SHELX etc. But how about  
programs in the Uppsala software factory etc?. Also is it difficult  
to install these programs - are there problems? Is linux still a  
safer choice?


sheemei


-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Biochemistry and Molecular Biology, W8708
615 North Wolfe Street
Baltimore, MD 21205
Phone: +1-410-614-4742

[ccp4bb] Invisible but intact disulphides?

[Derek Logan]

Hello everyone,

We are working on a protein in which a long loop is held in place by a  
disulphide bond. All the biochemistry and biophysics of this protein  
indicates that the disulphide bond should be intact, but we only see  
one end of it in the crystal structure. The protein has not been  
exposed to any reductants. The data were collected at a medium  
intensity synchrotron source (MAX-lab in Lund) and the total dose  
should thus not have been extremely high. We have even looked at maps  
calculated from the first half of the dataset (45 minutes exposure vs.  
90) and there is no difference. We have tried to react the free  
cysteine with 1mM MeHgCl2 and 10mM iodacetamide, to no avail. Thus we  
really think the disulphide is intact even in the crystal.


Has anyone seen a similar case, where all evidence pointed to an  
intact disulphide but it was not visible 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 for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] Art Robbins Phoenix User Group

[Derek Logan]

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 Robbins'  
Phoenix robot:


Would anyone be interested in joining a Phoenix robot user group/ 
bulletin board? Someplace where users would be able to discuss their  
experiences, as well as to learn from the experiences of others.


I will be tallying posted responses and be in contact with Art  
Robbins Instruments.


Cheers,
David Critton
Department of Molecular Biology, Cell Biology  Biochemistry
Brown University, Providence, RI

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

[Derek Logan]

There are still a limited number of places available at the Como  
Crystallography School in late September.


Visit the web site for the detailed program and registration details!  
The registration deadline

has been extended for the last time, to 16th September.

http://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, Sweden)


AIMS

The school focuses on the application of X-ray crystallographic  
methods to the study of biological macromolecules, with emphasis on  
the latest developments. The programme includes lectures on protein  
expression and purification, crystallisation, data collection and  
processing, synchrotron sources, phasing, phase improvement, model  
building, refinement and analysis of structural data. These methods  
sections will be complemented with seminars about new structures.  
Participants who are encouraged to present a poster; nine of the oral  
contributions will be selected from the poster abstracts.

[ccp4bb] Registration deadline for Como Crystallography School extended

[Derek Logan]

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. You are welcome to  
continue using the hotel booking form provided by Centro Volta, but  
they are unable to guarantee that you will get the room of your choice  
from now on.


Derek

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

[Derek Logan]

*** 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  
macromolecular crystallography methodology.


For more details and to register, please visit the web page:
www.crystallographyschool.org

DEADLINES
Registration: 24th July
Accommodation: 25th July
Abstracts: 28th August

PRELIMINARY PROGRAMME AND REGISTRATION
The meeting will last from after lunch (not provided) on Monday  
September 29th, 2008, to after lunch (provided) on Friday October 3rd.  
A strictly limited number of Ph.D. students will be eligible for  
financial support. Those wishing to apply for such subsidy should  
submit a short CV and motivation at the time of application. Poster  
and oral presentation abstracts should also be submitted before 28th  
August for inclusion in the abstract book.


PURPOSE AND ORGANIZATION OF THE SCHOOL
The school will be open to a maximum of 200 participants and will  
focus on the application of X-ray crystallographic methods to the  
study of proteins and nucleic acids, with emphasis on the latest  
developments. The program will include lectures on protein expression  
and purification, crystallization, data collection and processing,  
synchrotrons, phasing (MAD/SAD and molecular replacement), phase  
improvement, model building, refinement, analysis and validation of  
structural data. These methods sections will be complemented with  
seminars about new structures. Several contributions will come from  
participants who are encouraged to propose a title for a poster or  
oral contribution in their application.


LOCATION
The school will be held at Società del Casino, Como, Italy. (http://www.societadelcasino.com/ 
), which is located literally in the centre of Como, next to the  
cathedral. Como can be reached comfortably by train (30-40 min. from  
Milan; 3-4 hours from Zurich and Basel) or by car via the A9-E36  
motorway. There will be a conference dinner att Villa Geno (http://www.villageno.it 
).


INVITED LECTURERS INCLUDE
Imre Berger (EMBL Grenoble), Ian Berry (Oxford University), Gleb  
Bourenkov (EMBL Hamburg), Dominique Bourgeois (ESRF), Florian  
Brueckner (Gene Center Munich), Marek Brzozowski (York University),  
Martin Caffrey (University of Limerick), Liz Carpenter (Diamond Light  
Source), Kevin Cowtan (York University), Zbigniew Dauter (Argonne  
National Laboratory), Simon Davis (Oxford University), Valeria de  
Marco (NKI, Amsterdam), Raimund Dutzler (University of Zürich), Hans  
Eklund (Swedish Agricultural University, Uppsala), Paul Emsley (Oxford  
University), Robert Esnouf (Oxford University), Stephen Graham (Oxford  
University), Tim Grüne (Göttingen University), Udo Heinemann (PSF  
Berlin), Michael Hennig (Hoffmann laRoche), Rod Hubbard (Versalis),  
Mariusz Jaskolski (Adam Mickiewicz University, Poznan), Wolfgang  
Kabsch (MPI Heidelberg), Claude Lecomte (Université Henri Poincaré,  
Nancy), Andrew Leslie (MRC LMB, Cambridge), Joseph Luft (Hauptmann- 
Woodward Institute, Buffalo), Natalia Markova (iNovacia, Stockholm),  
Garib Murshudov (York University), Frank Niesen (SGC Oxford), Poul  
Nissen (Århus University), Martin Noble (Oxford University), Santosh  
Panjikar (EMBL Hamburg), Navraj Pannu (Leiden University), Chris  
Phillips (Pfizer), Simon Phillips (Leeds University), Randy Read  
(Cambridge University), Marc Ruff (IGBMC, Strasbourg), Elisabeth Sauer- 
Eriksson (Umeå University), Gebhard Schertler (MRC LMB, Cambridge),  
Clemens Schulze-Briese (SLS, Villigen), Irmgard Sinning (Heidelberg  
University), Bente Vestergaard (Copenhagen University), Gert Vriend  
(Nijmegen University), Martin Walsh (MRC France, ESRF), Martyn Winn  
(STFC Daresbury Lab), Peter Zwart (Lawrence Berkeley Laboratory)

[ccp4bb] Postdoctoral position at Lund University

[Derek Logan]

Dear colleagues,

A postdoctoral position in Structure, function and dynamics of  
bacterial systems involved in sensing and adaptation to redox stress  
is available at Lund University. The project is a collaboration  
between the groups of Dr. Claes von Wachenfeldt at the Dept. of 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 structural biology, including the MAX-lab synchrotron  
with its nanovolume crystallisation facility. For more information, see:


The University: http://www.lu.se
Centre for Molecular Protein Science: http://www.mps.lu.se
Dept. of Cell and Organism Biology: http://www.cob.lu.se/engindex.html
Structural Biology at MAX-lab: http://cassiopeia.maxlab.lu.se

Derek
_
Derek Logan  tel: +46 46 222 1443
Associate professor  fax: +46 46 222 4692
Molecular Biophysics mob: +46 76 8585 707
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden

[ccp4bb] Weakest protein-protein complex crystallised: summary

[Derek Logan]

Hi,

Many thanks to all who replied to my enquiry about the weakest protein- 
protein complex crystallised. The idea that crystals themselves are  
weak complexes had already crossed my mind and I was glad to hear it  
confirmed by others. My impression is that there are no hard and fast  
rules, and that crystallisation conditions can both work in favour of  
and against the formation of complexes of many different affinities.  
However one should certainly not be discouraged from trying to  
crystallise complexes with Kd in the high uM or mM range. The one I  
was considering has Kd around 25 uM. Thanks for all the literature  
tips, which I will follow up (eventually).


One colleague, who naturally wishes to remain anonymous, suggested the  
recent controversial C3b structure as a candidate for the weakest  
complex yet crystallised. I think there was a play on words  
involved ;-) 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: +46 76 8585 707
Lund University, Box 124, 221 00 Lund, Sweden

Re: [ccp4bb] Friedel vs Bijvoet

[Derek Logan]

- 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 word...) the  
Röntgen moniker has stuck here in northern Europe too: in Swedish:  
Röntgenstrålning, in Danish and Norwegian: Røntgenstråling, in Dutch:  
Röntgenstraling. Also thanks to Wikipedia, I can inform you that it's  
called Röntgengeislun in Icelandic and Röntgensäteily in Finnish.  
Eastern Europe seems to have adopted various forms based on Rentgen,  
but I won't pretend I knew that before 5 minutes ago ;-)


Derek




- When the largest protein ever was discovered, it was called  
connectin, but a subsequent paper called it titin and the second  
name has stuck.  I actually can't remember who the connectin guy  
was ...


- When Joseph Fourier discovered that heat radiated from the earth  
could be reflected back by gasses in the atmosphere, he simply named  
it by describing it (in French).  Now this is (incorrectly) called  
the greenhouse effect.  Why not the Fourier effect?  Fortunately  
for Fourier, a mathematical series was named after him, although he  
neither discovered it (Budan did that), nor implemented it (Navier  
did that).  All Fourier did was present a theorem based on a flawed  
premise that turned out to be right anyway.


So, I decided to look up Friedel and Bijvoet in the Undisputed  
Source of All Human Knowledge (wikipedia) and found that Friedel's  
Law ... is a property of Fourier transforms http://en.wikipedia.org/wiki/Fourier_transform 
 of real functions.


I am willing to believe that.  And considering this origin I would  
think it appropriate to call (hkl) and (-h-k-l) a Friedel pair (or  
Friedel's pair as it is described in the USAHK).  G. Friedel was  
indeed a crystallographer, but I doubt he considered more than this  
simple centrosymmetric property.  Who would care in 1913 which is F+  
and F-?  The atomic scattering factors had not yet been worked out  
at that time.  Ewald may have predicted it, but anomalous scattering  
was not shown to exist until the classic work of Koster, Knol and  
Prins (1930).  I guess that goes to show that if you want something  
named after you... keep it at one or two authors.


Perhaps it has to do with the original paper getting old enough that  
it gets too hard to find.  I'm sure in G. Friedel's paper in 1913 he  
cited Joseph Fourier's Paper from 1822.  Or did he?  I wonder if  
they were already calling it a Fourier Transform at that time?


Okay, so what, exactly did Bijvoet do?  Everyone cites his Nature  
paper (1951), but one thing that I was NOT KIDDING about in my April  
Fool's joke was that this paper (like so many other high-profile  
papers) contains almost no information about how to reproduce the  
results.  I was also not kidding that boring little details like the  
reasoning behind the conclusion (the hand of the microworld) were  
relegated to a more obscure journal (the one in the Proc. Royal.  
Soc. Amsterdam).  I WAS kidding about having found and read that  
paper.  I have never seen it.  Still, Bijvoet did the first  
experiment to elucidate the absolute configuration, and he  
definitely deserves credit for that.
So, particularly in that light, I would agree that any pair of  
reflections that would be equivalent if not for anomalous scattering  
effects could be called a Bijvoet pair.  This is because they  
contain the information needed to apply Bijvoet's technique.
Something that has always eluded me is who decided which is F+ and  
F-?  After all, the reciprocal lattice is very very nearly  
centrosymmetric.  You cannot tell by looking at a single diffraction  
image whether that spot at a given X,Y pixel coordinate is F+ or F-,  
you need to know the axis convention of the camera.  At some point  
in writing the CCP4 libraries with their asymmetric unit  
definitions, someone must have established a convention.  What is  
it?  To me, the reasoning behind these assignments is, in fact, they  
key to assigning the absolute configuration, not the anomalous  
scattering effect itself.  So, who worked this out?  Should we  
really be calling them Dodson pairs?


-James Holton
MAD Scientist

[ccp4bb] Weakest protein-protein complex crystallised

[Derek Logan]

Hi,

Can anyone advise me what is currently the weakest protein-protein  
complex yet crystallised? Google searching turned up a paper from the  
Tromsø crystallography group (Helland et al. 1999, JMB 287, 923–942)  
in which a complex between beta-trypsin and a P1 mutant of BPTI with a  
Kd 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 46 222 1443
Associate professor  fax: +46 46 222 4692
Molecular Biophysics mob: +46 76 8585 707
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden

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

[Derek Logan]

*** REMINDER ***

REGISTRATION IS OPEN
for the Ninth International School on the Crystallography of  
Biological Macromolecules

Como (Italy), 29th September – 3rd October 2008

for more details and to register, please visit the web page:
www.crystallographyschool.org

DEADLINES
Registration: 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 meeting will last from after lunch (not provided) on Monday  
September 29th, 2008, to after lunch (provided) on Friday October 3rd.  
A strictly limited number of Ph.D. students will be eligible for  
financial support. Those wishing to apply for such subsidy should  
submit a short CV and motivation at the time of application. Poster  
and oral presentation abstracts should also be submitted before 28th  
August for inclusion in the abstract book.


PURPOSE AND ORGANIZATION OF THE SCHOOL
The school will be open to a maximum of 200 participants and will  
focus on the application of X-ray crystallographic methods to the  
study of proteins and nucleic acids, with emphasis on the latest  
developments. The program will include lectures on protein expression  
and purification, crystallization, data collection and processing,  
synchrotrons, phasing (MAD/SAD and molecular replacement), phase  
improvement, model building, refinement, analysis and validation of  
structural data. These methods sections will be complemented with  
seminars about new structures. Several contributions will come from  
participants who are encouraged to propose a title for a poster or  
oral contribution in their application.


LOCATION
The school will be held at Società del Casino, Como, Italy. (http://www.societadelcasino.com/ 
), which is located literally in the centre of Como, next to the  
cathedral. Como can be reached comfortably by train (30-40 min. from  
Milan; 3-4 hours from Zurich and Basel) or by car via the A9-E36  
motorway. There will be a conference dinner att Villa Geno (http://www.villageno.it 
).


INVITED LECTURERS INCLUDE
Imre Berger (EMBL Grenoble), Ian Berry (Oxford University), Gleb  
Bourenkov (EMBL Hamburg), Dominique Bourgeois (ESRF), Florian  
Brueckner (Gene Center Munich), Marek Brzozowski (York University),  
Martin Caffrey (University of Limerick), Liz Carpenter (Diamond Light  
Source), Kevin Cowtan (York University), Zbigniew Dauter (Argonne  
National Laboratory), Simon Davis (Oxford University), Valeria de  
Marco (NKI, Amsterdam), Raimund Dutzler (University of Zürich), Hans  
Eklund (Swedish Agricultural University, Uppsala), Paul Emsley (Oxford  
University), Robert Esnouf (Oxford University), Stephen Graham (Oxford  
University), Tim Grüne (Göttingen University), Udo Heinemann (PSF  
Berlin), Michael Hennig (Hoffmann laRoche), Rod Hubbard (Versalis),  
Mariusz Jáskolski (Adam Mickiewicz University, Poznan), Wolfgang  
Kabsch (MPI Heidelberg), Claude Lecomte (Université Henri Poincaré,  
Nancy), Andrew Leslie (MRC LMB, Cambridge), Joseph Luft (Hauptmann- 
Woodward Institute, Buffalo), Natalia Markova (iNovacia, Stockholm),  
Garib Murshudov (York University), Frank Niesen (SGC Oxford), Poul  
Nissen (Århus University), Martin Noble (Oxford University), Santosh  
Panjikar (EMBL Hamburg), Navraj Pannu (Leiden University), Chris  
Phillips (Pfizer), Simon Phillips (Leeds University), Randy Read  
(Cambridge University), Marc Ruff (IGBMC, Strasbourg), Elisabeth Sauer- 
Eriksson (Umeå University), Gebhard Schertler (MRC LMB, Cambridge),  
Clemens Schulze-Briese (SLS, Villigen), Irmgard Sinning (Heidelberg  
University), Bente Vestergaard (Copenhagen University), Gert Vriend  
(Nijmegen University), Martin Walsh (MRC France, ESRF), Martyn Winn  
(STFC Daresbury Lab), Peter Zwart (Lawrence Berkeley Laboratory)

Re: [ccp4bb] Help with pseudosymmetry problem

[Derek Logan]

Hi Peter,


Can you try to run xtriage and see what it tells you in terms of
possible twin laws and merging statistics in higher symmetry space
groups?


The log file is attached. xtriage does not find any clear signs of  
pseudosymmetry or higher metric symmetry, but it does detect the  
pseudo-translation peak at  (0.129, 0.475, 0.218) with 10% of the  
origin height, which it doesn't consider as significant (I get 20%  
when I do it using FFT)



If for some reason no twin laws are found, you can manually change the
unit cell on the command line to have beta exactly equal to 90...


I didn't do this, as possible twin law was found. Or have I  
misunderstood the logic?



Let me know what the logfile tells you. If the translation is
'special' xtraige will tell you what the approximate pseudo symmetry
would be.


It doesn't seem to think so.

Derek

P.S. 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 spherical polars. The space group is P21 with beta = 92.2°.  
The

kappa=180° section of the SRF, calculated using Molrep, is at

http://mole.mbfys.lu.se/~derek/selfRF_180.png

and contains two big peaks around 7 sigma. I'm having trouble  
identifying

these in the list of peaks from Molrep:

   thetaphi chialphabeta   gamma Isym_i
Isym_j
Sol_RF   1  0.000.000.00  0.000.000.00
1   1
Sol_RF   1 90.00  -90.00  180.00  0.00  180.000.00
1   2
Sol_RF   1 90.00   90.00  180.00  0.00  180.000.00
2   1
Sol_RF   1  0.000.000.00  0.000.000.00
2   2
Sol_RF   2158.56  180.00  180.00  0.00   42.89 -180.00
1   1
Sol_RF   2111.440.00  180.00   -180.00  137.110.00
1   2
Sol_RF   2111.440.00  180.00180.00  137.110.00
2   1
Sol_RF   2 21.440.00  180.00180.00  -42.890.00
2   2
Sol_RF   3165.650.00  180.00   -180.00   28.700.00
1   1
Sol_RF   3104.35 -180.00  180.00  0.00  151.30  180.00
1   2
Sol_RF   3104.35  180.00  180.00  0.00  151.30 -180.00
2   1
Sol_RF   3 14.35 -180.00  180.00  0.00  -28.70  180.00
2   2


It seems to me to be two copies of peak 2. I believe theta starts  
in the
middle, perpendicular to the page and phi starts on the x axis,  
thus the
peak just below the centre would be (21.44, 0, 180). I presume that  
the
second peak is the symmetry-related (158.56, 180, 0)? However where  
is
(111.44 0 180)? I would expect to see this near the bottom of the  
plot, but

it's not there. I'm sure I'm missing something fundamental about the
symmetry of the SRF projection, but unfortunately I don't have a  
supervisor

to bug about this (I *am* the supervisor...)

In the native Patterson

http://mole.mbfys.lu.se/~derek/nativePatterson.png

there are two peaks of almost equal height. How can this be  
reconciled with
having only one strong peak in the SRF? There are most likely two  
dimers in
the asymmetric unit, but there may only be one, with very high  
resulting
solvent content. What's more the molecules are leucine-rich repeat  
proteins

and have weak internal symmetry. I believe this was an issue with the
ribonuclease inhibitor, but looking briefly at the crystallisation  
article

and structure article I wasn't able to find a rationalisation of this
problem. The 2-fold is perpendicular to b*. How could this cause  
the two

peaks?

Thanks
Derek




--
-
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
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[ccp4bb] Help with pseudosymmetry problem

[Derek Logan]

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 at


http://mole.mbfys.lu.se/~derek/selfRF_180.png

and contains two big peaks around 7 sigma. I'm having trouble  
identifying these in the list of peaks from Molrep:


thetaphi chialphabeta   gamma  
Isym_iIsym_j

Sol_RF   1  0.000.000.00  0.000.000.00   1   1
Sol_RF   1 90.00  -90.00  180.00  0.00  180.000.00   1   2
Sol_RF   1 90.00   90.00  180.00  0.00  180.000.00   2   1
Sol_RF   1  0.000.000.00  0.000.000.00   2   2
Sol_RF   2158.56  180.00  180.00  0.00   42.89 -180.00   1   1
Sol_RF   2111.440.00  180.00   -180.00  137.110.00   1   2
Sol_RF   2111.440.00  180.00180.00  137.110.00   2   1
Sol_RF   2 21.440.00  180.00180.00  -42.890.00   2   2
Sol_RF   3165.650.00  180.00   -180.00   28.700.00   1   1
Sol_RF   3104.35 -180.00  180.00  0.00  151.30  180.00   1   2
Sol_RF   3104.35  180.00  180.00  0.00  151.30 -180.00   2   1
Sol_RF   3 14.35 -180.00  180.00  0.00  -28.70  180.00   2   2

It seems to me to be two copies of peak 2. I believe theta starts in  
the middle, perpendicular to the page and phi starts on the x axis,  
thus the peak just below the centre would be (21.44, 0, 180). I  
presume that the second peak is the symmetry-related (158.56, 180, 0)?  
However where is (111.44 0 180)? I would expect to see this near the  
bottom of the plot, but it's not there. I'm sure I'm missing something  
fundamental about the symmetry of the SRF projection, but  
unfortunately I don't have a supervisor to bug about this (I *am* the  
supervisor...)


In the native Patterson

http://mole.mbfys.lu.se/~derek/nativePatterson.png

there are two peaks of almost equal height. How can this be reconciled  
with having only one strong peak in the SRF? There are most likely two  
dimers in the asymmetric unit, but there may only be one, with very  
high resulting solvent content. What's more the molecules are leucine- 
rich repeat proteins and have weak internal symmetry. I believe this  
was an issue with the ribonuclease inhibitor, but looking briefly at  
the crystallisation article and structure article I wasn't able to  
find a rationalisation of this problem. The 2-fold is perpendicular to  
b*. How could this cause the two peaks?


Thanks
Derek

Re: [ccp4bb] Help with pseudosymmetry problem

[Derek Logan]

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 your 2 fold is in the a c* plane,  
21 degrees or 111 degrees from c*.

The 2 peaks you see are symmetry equivalents.


This was my interpretation. Glad we agree ;-) The documentation says  
A parallel to X , Cstar parallel to Z


As  for the Patterson - what height are those peaks relative to the  
origin?


The peaks are  u = 0.129, v = 0.473, w = 0.220 (20% of origin peak  
height) and u = 0.180, v = 0.500, w = 0.248 (19%). What I don't get is  
why there are two and only one strong 2-fold. 2 dimers in the AU gives  
50% solvent, 1 dimer 75%. The crystals diffract to 2.3Å, which would  
tip the balance in favour of 50% solvent in my opinion.


With 2 dimers in the asymm unit and with the non-cryst 2-fold  
perpendicular to b* you could have such translations between one  
monomer and another.


Would the 2-folds of both dimers have to be very similarly oriented?  
Maybe one peak masks the other at this resolution?


is there a model - easiest to solve it then analyse this sort of  
stuff later!


Believe me, we've been trying for a very long time! The problem is  
that it's a leucine rich repeat protein with under 30% sequence  
identity to any of the other LRR models out there. I think the failure  
of MR is down to a combination of a) the low homology, b) the  
pseudosymmetry, c) the nature of the LRR, which means you can get MR  
solutions that are out by one or more repeats. Maybe even the internal  
symmetry of the whole LRR structure can add to this pathology? We've  
had some solutions that looked almost right, but we can never see much  
more than what's already in the MR solution.


Ian wrote:

The symmetry of the self-RF is explained in detail in the  
documentation for POLARRFN, in fact I would advise you to use this  
because you can then plot monoclinic space groups with the unique b  
axis along the orthogonal Z axis (NCODE = 3) and then the symmetry  
is *much* easier to interpret.


The reason I started using Molrep was that POLARRFN always used to  
choke on these data. However that problem seems to have disappeared.  
Using ORTH 3 indeed gives a more interpretable plot, as you say.


According to polarrfn.doc the symmetry generated by a 2-fold along b  
parallel to Z is (180-theta, 180-phi, kappa) so the peak in the list  
(159,180,180) is the same as (21,0,180) which is a NCS 2-fold that  
you can see just below centre.  The peak (111,0,180) is thus the  
same as (69,180,180) near the top which is another NCS 2-fold perp  
to the first generated by the crystallographic 2-fold.


Indeed, I see the peak (69, 180, 180) but I don't find it in the list  
in the log file from Molrep. I thought that list was supposed to be  
exhaustive. Also the plot is not well documented for Molrep. I wrote  
to the BB a while ago to ask what the contour levels were but no-one  
answered. By Googling I found a crystallisation paper where it was  
described as from 0.5 sigma in steps of 0.5 sigma but that  
information appears to have come by word of mouth. Also, is it just  
the north hemisphere, as Claudine put it, that is plotted?


Anyway, I feel somewhat wiser now...

Derek

[ccp4bb] Merging CCP4i projects from two computers

[Derek Logan]

Hi everyone,

I've been working on a project using CCP4i on two separate computers  
in parallel and now unfortunately have jobs spread over the two  
locations. I would now like to consolidate these. Some of the new jobs  
on one computer will have the same run number as different ones 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 8585 707
Box 124, Lund, Sweden

[ccp4bb] Thermofluor again

[Derek Logan]

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

[Derek Logan]

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  
away. We chose the Stratagene for a couple of reasons:


a) the iQ5 required a manual change of filter which would make it  
unuseable for qPCR, and while we don't anticipate a great deal of  
usage for qPCR it would be a shame to cripple such an expensive  
machine. The filter for the Mx3005p can be chosen in software.
b) the Mx3005p uses a photomultiplier instead of a CCD to read the  
plate. This (according to Stratagene) leads to better uniformity of  
detection across the plate. I believe the iQ5 requires some kind of  
calibration run each time you use it.


Our first impression of the Stratagene software is very positive. We  
haven't tried the iQ5 but others say it's a perfectly fine machine. A  
couple of people who know more than most are Helena Berglund at SGC  
Stockholm (BioRad) and Frank Niesen at SGC Oxford (Stratagene).  
Whichever of these two machines you choose, SGC have produced an  
excellent detailed protocol and from their FTP site ftp.sgc.ox.ac.uk  
you can download Excel spreadsheets to calculate Tm and produce at-a- 
glance output for up to 96 wells from either iQ5 or Mx3005p output.  
SGC intend to continue supporting output from both machines.


There are cheaper models by BioRad which we didn't look into (we got a  
grant for the Mx3005p!) but I imagine they have sensitivity/wavelength  
issues.


The link to the SGC protocol is:

http://www.ncbi.nlm.nih.gov/pubmed/17853878?ordinalpos=3itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

HTH
Derek

On Feb 12, 2008, at 18:07, mesters wrote:

Sorry for the off-topic but can somebody recommend highly a  
sensitive RT-PCR machine for the thermofluor experiment (sypro  
orange).
That would imply excitation below 500 nm (ideally 470) and detection  
at about 570 nm, right? I know several simple machines have a  
problem with the 570 nm...


Jeroen.

--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: [EMAIL PROTECTED]
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)
--

[ccp4bb] Default contour levels for SRF in Molrep

[Derek Logan]

Hi,

What are the default contour levels for the Postscript plot of the  
self rotation function produced by Molrep? They are not specified in  
the documentation but Googling turns up a couple of articles where the  
levels are described as from 0.5 sigma above the mean in steps of 0.5  
sigma. 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

[Derek Logan]

Hi,

I'd like to find out how successful the quick soak method for heavy  
atom derivatisation proposed by Radaev and Sun:


Sun PD, Radaev S, Kattah M. Generating isomorphous heavy-atom  
derivatives by a quick-soak method. Part I: test cases. Acta Cryst.  
2002. D58:1092-1098.


has been in comparison to the classical method of longer soaks at  
low concentrations of heavy atom compound. The method was quite  
successful in our hands a few years ago but (fortunately?) it's  
becoming increasingly rare that we use heavy atoms. I understand that  
evidence 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

[ccp4bb] xplot84driver problems

[Derek Logan]

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 file on the command line using pltdev then  
use Preview to view the PS as PDF, rather than just using the CCP4i  
pulldown menu.


Initially xplot84driver complains that libifcore.dylib is missing.  
This appears to be an Intel compiler-specific library which I just  
happen to have in /opt/intel/fc/9.1.024/lib, as I once evaluated the  
beta release of the compiler. If I copy this to $CCPLIB or link from  
there to it, it complains that it doesn't have libifm.dylib, which in  
turn complains that it doesn't have libirc.dylib. Finally when all  
these libraries are linked to and loaded, xplot84driver complains  
about Bad plot84 file 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

Re: [ccp4bb] xplot84driver problems

[Derek Logan]

Hi,

Yes, I made the files on the Intel Mac. I've sent one to Charles  
Ballard for testing. They do also work wih pltdev. I agree about the  
antediluvial origins of xplot84driver, but for lack of anything  
better...


Derek

On Sep 6, 2007, at 17:15, [EMAIL PROTECTED] wrote:



Did you make your plt file on the intel mac?  I've noticed that  
ones I made on ppc give that error on my otherwise functional  
xplot84driver (in the fink package).


I tried byte-swapping with dd but to no avail.

I guess this is still the cutting edge of 1984 software?

Bill

On Thu, 6 Sep 2007 15:02:01 +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 to convert every plot file on the command line using  
pltdev then
 use Preview to view the PS as PDF, rather than just using the  
CCP4i

 pulldown menu.

 Initially xplot84driver complains that libifcore.dylib is  
missing.
 This appears to be an Intel compiler-specific library which I  
just
 happen to have in /opt/intel/fc/9.1.024/lib, as I once  
evaluated the
 beta release of the compiler. If I copy this to $CCPLIB or  
link from
 there to it, it complains that it doesn't have libifm.dylib,  
which in
 turn complains that it doesn't have libirc.dylib. Finally when  
all

 these libraries are linked to and loaded, xplot84driver complains
 about Bad plot84 file 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

Re: [ccp4bb] AKTA prime

[Derek Logan]

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 tel: +46 46 222 1443
Associate professor fax: +46 46 222 4692
Molecular Biophysics
Lund University
Box 124, Lund, Sweden


On Feb 13, 2007, at 23:16, Frank Lee wrote:



Dear all,

I need to decide between buying an AKTA prime and an AKTA FPLC from  
GE health care. I understand AKTA prime is a low-pressure system,  
but because it is too much cheaper than AKTA FPLC, it is still very  
attractive to me.


I will mainly use it for Nickel columns and gel filtration columns,  
and I am worried about the latter. Is it true that using AKTA  
prime, you can only run the 24 ml Superdex 200 column at 0.1 or 0.2  
ml/min?


Could anyone who has used AKTA prime give me some feedbacks? I  
would appreciate it.


Best,
Frank

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