[ccp4bb] Install CCP4 on MacOS Monterey

[Klaus Futterer]

I am trying to install CCP4 on MacOS 12.7 (Monterey).

Unfortunately, the disk image (ccp4 8.0) does not open, despite me following 
the advice of Ctrl-Click, open ... all I get is the informative window with the 
instructions how to launch the disk image for MacOS 10.15 and later.

Any advice out there for me?

Klaus

===
Klaus Fütterer, PhD
Reader in Structural Biology


School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UK(voice mail messages will 
forward to my email inbox)

My normal working hours are Mon - Fri 9.00 - 6.00 pm.
For my office hours, please contact me by email

How to pronounce my 
name

===



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[ccp4bb] Postdoc in the group of Aneika Leney at U. Birmingham

[Klaus Futterer]

Please, see the postdoctoral position advertised below in the broad context of 
structural biology research using mass spectrometry.

For informal inquiries contact my colleague Dr Aneika Leney (a.le...@bham.ac.uk)

Klaus

===
Klaus Fütterer, PhD
Reader in Structural Biology


School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UK(voice mail messages will 
forward to my email inbox)

My normal working hours are Mon - Fri 9.00 - 6.00 pm.
For my office hours, please contact me by email

How to pronounce my 
name

===

From: Aneika Leney (Biosciences) 
Sent: 18 March 2024 13:31

Hi all,

We are currently advertising a 3-year post-doc position. 
https://www.jobs.ac.uk/job/DGL324/research-fellow-in-structural-biology. I'm 
looking for either a structural biologist or a mass spectrometrist (or someone 
with both expertise). They would work on finding a new molecular switch to 
enhance photosynthetic control.

Thanks,

Aneika





Dr Aneika Leney
Associate Professor in Biomolecular Mass Spectrometry
School of Biosciences
College of Life and Environmental Sciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT, UK





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Re: [ccp4bb] X-ray crystallography defense questions

[Klaus Futterer]

Q1: who needs X-ray crystallography - we have cryoEM?


Q2: what's the phase problem and is it still a problem (after so many years)?


;-)




===
Klaus Fütterer, PhD
Reader in Structural Biology


School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UK(voice mail messages will 
forward to my email inbox)

My normal working hours are Mon - Fri 8.30 - 5.30 pm.


===

From: CCP4 bulletin board  on behalf of 
jbesaw1...@gmail.com 
Sent: 14 June 2022 16:58:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] X-ray crystallography defense questions

Hello CCP4!

I am preparing for my PhD defense on X-ray crystallography of membrane proteins.

So my ask from you folks is: What X-ray crystallography questions would you ask 
in a PhD defense?

All questions - easy, tough, tricky - are welcome.

Thank you kindly,

Jessica Besaw






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[ccp4bb] Research Associate in Integrated Structural Biology at University of Birmingham

[Klaus Futterer]

Dear colleagues,


Prof Teresa Carlomagno has recently joined the School of Biosciences at the 
University of Birmingham and is in the process of establishing a new research 
group in integrated structural biology. Part of that group is the position of a 
Research Associate position described below.


Full details can be found at: 
https://www.jobs.ac.uk/job/CKC707/research-associate


For informal inquiries, please contact Teresa directly at 
t.carloma...@bham.ac.uk.


Thank you.


Klaus





Research Associate
School of Biosciences
College of Life and Environmental Sciences

Location: University of Birmingham, Edgbaston, Birmingham UK


Full Time FTC for 5 years

Closing date – 30.11.2021



Role/Project Background
The research group to which the post is associated uses integrative structural 
biology to understand functional mechanisms of proteins, nucleic acids and 
their complexes. The Research Associate will express and purify functional 
proteins, produce nucleic acids either by in vitro transcription or chemical 
synthesis, reconstitute large biomolecular particles from recombinant material, 
study the biomolecular complexes with biophysical and biochemical experiments 
and establish functional tests in vitro. The material produced and studied by 
the Research Associate will then be used for structural biology experiments. 
The day-to-daywork includes cloning, bacterial cell culture, protein expression 
and purification, RNA transcription and purification, RNA and protein 
engineering, biophysical studies of biomolecules and of their mutual 
interactions, for example through Isothermal Titration Calorimetry, Multiple 
Angle Light Scattering and Electrophoretic Mobility Assays. In addition, the RA 
will help with laboratory management tasks.


Main duties

  *   •   Collect research data; this may be through a variety of research 
methods, such as scientific experimentation (as described above) and literature 
reviews
  *   •   Analyse research data as directed
  *   •   Present research outputs, including drafting academic 
publications or parts thereof, for example at seminars and as posters
  *   •   Develop or adapt techniques, models and methods
  *   •   Provide guidance as required to support staff and any students 
who may be assisting with research
  *   •   Deal with problems that may affect the achievement of research 
objectives and deadlines
  *   •   Carry out administrative tasks related directly to the delivery 
of the research
  *   •   Promote equality and values diversity acting as a role model and 
fostering an inclusive working culture

Person Specification

•  Degree or equivalent in Biochemistry, Biophysics or Molecular Biology

•  Proficiency in protein recombinant expression and purification and/or in 
RNA synthesis and purification

•  Practical experience in a biochemical laboratory

•  Experience in some of the biophysical techniques mentioned above

•  Skills in analysing data

•  Ability to analyse information and communicate effectively

•  Ability to access and organise resources successfully

•  Knowledge of the protected characteristics of the Equality Act 2010, and 
how to actively ensure in day-to-day activity in own area that those with 
protected characteristics are treated equally and fairly


===
Klaus Fütterer, PhD
Reader in Structural Biology


School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UK(voice mail messages will 
forward to my email inbox)

My normal working hours are Mon - Fri 8.30 - 5.30 pm.


===



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[ccp4bb] TBSGC web site

[Klaus Futterer]

Does anyone on the ccp4bb know whether the TBSGC site is still accessible 
somewhere?

Klaus

===
Klaus Fütterer, PhD
Reader in Structural Biology
(Office hours: Mon 5 - 6 pm, Fri 9.30 - 10.30 am)

School of Biosciences
LES CollegeEmail: 
k.futte...@bham.ac.uk
University of Birmingham Phone: +44 - 121 - 414 5895
Birmingham, B15 2TT, UKRoom 703 (7th floor)
===



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[ccp4bb] Recruitment in Structural Biology/Biophysics

[Klaus Futterer]

Dear All,

The College of Life and Environmental Sciences at the University of  
Birmingham is seeking to recruit a research group leader in  
structural biology or a related discipline. Individuals pursuing the  
study of structure-function relationships in the context of membrane  
transport or transmembrane signalling are particularly welcome to  
apply. Successful applications will be able to demonstrate research  
endeavour at the highest standing and a proven record of teaching at  
all relevant levels.


Further details can be found at http://www.biosciences.bham.ac.uk/ 
NewAppointments/New_Appointments.htm.
Informal enquiries should be directed to Prof. Kevin Chipman, Head of  
School of Biosciences, 0121-414 5422 or j.k.chip...@bham.ac.uk.





-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: k.futte...@bham.ac.uk
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

Re: [ccp4bb] RAxis & fiber diffraction

[Klaus Futterer]

Sue,

Louise Serpell at the University of Sussex, UK specialises on fibre  
diffraction and has some neat software that may be useful to your cause.

You can contact her at [EMAIL PROTECTED]

Klaus



-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


On 26 Nov 2008, at 03:08, Sue Roberts wrote:


Hello Everyone

Since I'm convinced that ccp4bb is the repository of all knowledge  
about all diffraction phenomena...


A colleague would like to do some fiber diffraction studies.  I  
have an RAxis - I know we can put the fiber in the beam and shoot  
it and get some pattern on the detector.


Can anyone recommend some reading material or tutorials for me to  
learn more about what I've agreed to do?


Assuming the material is actually crystalline enough to give a  
pattern on the detector, I can pick peaks and get d-spacings.   
What  more sophisticated, readily available methods (software?) is  
out there for, perhaps, data reduction (if there is such a thing  
for fiber diffraction) or subsequent analysis.


Thanks,

Sue

Sue Roberts
Department of Biochemistry & Molecular Biophysics
University of Arizona
[EMAIL PROTECTED]520 621-8171

[ccp4bb] Summary of Crystal Imaging Systems

[Klaus Futterer]

Summary on Crystal Imaging equipment

First, I would like to point out that the replies I received do not  
amount to a representative survey that would accurately reflect the  
performance of the instruments mentioned. Not all users of crystal  
imaging system users read the BB, disappointed users may be more  
likely to respond and their testimony might reflect out-of-date  
versions, happy users may not have the time or inclination to express  
their views (they are probably busy mounting their crystals), and  
most replies reported on specific aspects of the experience a  
particular user has had. (Ok - I hope this disclaimer will cover any  
legal issues).



CrystalPro - (3 responses; made by Tritek, distributed by Molecular  
Dimensions)
Response 1 described software as not user-friendly and indicated that  
the instrument, as a result, found little use in the lab (did not  
say, whether this was a recent experience).
Response 2 – described hardware problems and software bugs (since  
then fixed). Image quality and brightness was described as wanting.
Response 3 – described image quality as sufficient, did not log any  
specific complaints.


Rhombix Vision -  (1 response, instrument longer sold, used to be  
distributed by Thermo)
Response noted very good imaging quality, good reliability, no  
service issues


RockImager - (4 responses, made/distributed by Formulatrix)
Favourable reviews throughout for imaging quality and reliability.  
Service by company was reported as prompt and effective. Temporary  
condensation problems (resolved) were mentioned in context of the 4ºC  
incubator.


Crystal Farm - (1 response, made/distributed by Bruker AXS)
Response was unfavourable. Noted reliability and service issues.  
Imaging quality was not described in this response.


Minstrel - (1 response, made/distributed by Rigaku)
Response described instrument as having very good image quality, easy- 
to-use software, and reported no problems with the instrument (was  
installed only 4 months ago).


CrysCam - (2 responses, made by Art Robbins Instruments, distributed  
in Europe by Dunn Labortechnik)
Response 1 – favourable (but by admission of the author biased).  
Described the instrument as simple, robust and inexpensive.

Response 2 – noted low resolution and "poor optics".
(CrysCam is a stand-alone desktop instrument w/o incubator/hotel)

Klaus



-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

[ccp4bb] Opinions on Crystal Imaging Systems

[Klaus Futterer]

Dear CCP4BB community,

We are looking into acquiring a crystal imaging system. I'm keen to  
learn about personal preferences and experiences, perhaps with some  
technical performance specifics. Points of interest include (but are  
not limited to)


* quality of images (focussing depth, lighting, ...)
* reliability
* service needs and serviceability
* drop localisation

Could I suggest to forward replies directly to [EMAIL PROTECTED]  
rather than to the BB so as not to upset any particular supplier  
unnecessarily?

(I promise to generate a posting-suitable summary).

Many thanks,

Klaus




-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

[ccp4bb] disulfide bond in coot

[Klaus Futterer]

Does anyone know how to prevent Coot from establishing a disulfide  
bond between two adjacent Cys residues?

I have reason to suspect that the bond is (at least partially) reduced.

Thanks.

Klaus





-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

[ccp4bb] Sequence of crystallised protein fragment

[Klaus Futterer]

We have a 150 kDa protein that reproducibly crystallises at one of  
the Hampton Screen conditions. However, we know from SDS gel analysis  
that the crystals contain only a 45 kDa fragment, that forms through  
proteolytic cleavage over time. We would like to determine the  
sequence boundaries of the fragment.


We believe a combination of N-terminal sequencing plus MS analysis  
might give us the information we need, but I was wondering whether  
the ccp4bb community has other suggestions.


Klaus






-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

Re: [ccp4bb] is it Ok to freeze

[Klaus Futterer]

"... room that was lined with insulated steel walls and that could be  
flushed with liquid nitrogen."


I'm trying to picture this ... did you guys have some kind of LN2- 
proof SCUBA diving equipment to work in there?


Klaus




-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


On 19 Jun 2008, at 18:04, Mischa Machius wrote:

Ha, everyone seems to be bragging about how far back cryo- 
crystallography really goes. In that vain, I'd like to mention  
that, in Martinsried, we had a room that was lined with insulated  
steel walls and that could be flushed with liquid nitrogen. It was  
requested (demanded, really...) by Robert Huber when the Max-Planck  
Institute was finalized in 1972 (I hope I got my history right).  
That room contained an entire diffraction system. Talk about  
crystal cooling... bah, way too dinky. Cool the entire room! Of  
course, it was a hazard to work in that room, and so - as far as I  
know - there was only one post-doc from India how ever used it.  
That room had an ante-room with two more generators plus detectors  
that could be cooled down to -20°C! Ah, the good old Wild West  
times of macromolecular crystallography...


Cheers - MM



On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote:


Well everyone, talking of early applications of cryocooling to X-ray
crystallography, what about Sten Samson's marvellous helium cryostat
which was operational at Caltech since the end of the 1970s and  
used to

reach temperatures around 20 K routinely , see for example:

Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4.
Structure of a B-DNA dodecamer at 16 K.
Drew HR, Samson S, Dickerson RE.

That instrument (and its twin) are now both with Riccardo Destro in
Milano.

Ciao!

Pietro




--
Pietro Roversi
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3RE, England UK
Tel. 0044-1865-275385



-- 
--

Mischa Machius, PhD
Associate Professor
Department of Biochemistry
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353

Re: [ccp4bb] discontinuous data wedges in XDS

[Klaus Futterer]

Is it not sufficient to first integrate the one wedge, then use this  
wedge

as a reference data set when integrating the second one?
(REFERENCE_DATA_SET= ../wedge01/XDS_ASCII.HKL)

Klaus




-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


On 29 Apr 2008, at 22:57, Juergen Bosch wrote:

You can integrate them as separate wedges (in different  
directories), then later merge them (XDS_ASCII.HKL) in Xscale. Make  
sure though you have the orientation right and starting angles etc.
You'll have to first refine one wedge, then once you are happy with  
it copy the GXPARM.XDS into the other directories (as XPARM.XDS)  
and input those parameters into XDS..INP


Juergen

Van Den Berg, Bert wrote:


Hi all,

is it possible to input discontinuous data wedges into XDS  
(obtained from for example inverse beam sweeps)? (So wedge se1  
goes from 0-90 deg (image 1-90), se2 from 180-270 (image 1-90),  
etc). Or do I have to rename everything so that I get one data  
file in which the rotation ranges are continuous?


Thanks, Bert

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm




--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

[ccp4bb] SUMMARY: update of coot via fink

[Klaus Futterer]

Problem was solved by

fink selfupdate
fink update-all

Thanks to Chris Richardson, who suggested the above, and Andreas  
Förster,

who suggested to be patient when launching updated coot the first time.


Klaus



-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

[ccp4bb] upgrade coot via fink on OS X

[Klaus Futterer]

I had previously installed coot 0.3.2 using fink on OS X on MacBook Pro
(under Tiger).

Trying to update coot using fink proved more difficult.

Initially I tried
sudo apt-get install coot

Coot would install but would not start due to a library version  
mismatch.
Then it got messy. I followed instructions given on Bill Scott's  
'Install crystallography using fink'

page:

fink scanpackages; fink index
sudo apt-get update
sudo apt-get dist-upgrade

The last command stalled - during imagamagick update.

Then I just tried again:
sudo apt-get install coot

Now coot would start, but stall saying:
Reading coordinate file: /sw/share/coot/standard-residues.pdb
 PDB file /sw/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
art_render_invoke: no image source given

Can anyone suggest to properly update fink and coot?

Thanks in advance,

Klaus



-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-

Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

[Klaus Futterer]

Christoph Gille's program STRAP generates structure-based multiple  
sequence alignment,
which can be combined with sequences for which no structure is  
available.


http://www.charite.de/bioinf/strap/


Klaus




-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


On 5 Dec 2007, at 05:03, david wu wrote:


Hi all，

I want to produce structure-based multiple sequence alignment of my  
protein with five of its homologs on DALI server. However, when I  
tried the "Database Search Form", only one homolog was picked up  
from PDB. If I align my protein with each homolog by the "DaliLite  
Pairwise comparison", how can I combine them together?


Thanks in advance.


Best regards,

Sincerely,

Dalei Wu
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
555 Zu Chongzhi Road, Shanghai, 201203, China
[EMAIL PROTECTED]
2007-12-05

Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface

[Klaus Futterer]

Deep-View (Swiss PDB Viewer) allows to calculate (and visualise) a  
'contact surface'

between two subunits, by loading the subunits into different layers.
Residues contributing to the contact surface can be selected by CTRL- 
click

on the contact surface line in the 'Cavities' menu, available under
the 'Window' drop-down menu.

BTW: I'm wondering about the 4A cut-off. Do distances greater than  
this not

matter anymore in the view of a 'pharmaceutical' crystallographer?

Klaus



-

Klaus Fütterer, Ph.D.

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
-


On 20 Sep 2007, at 20:29, Soisson, Stephen Michael wrote:

If you just want the residues involved in the interface, you can  
use the

byres selection commands in Pymol.

select contacts, (byres monA and (monB around 4))

which will show all the residues on monA that are within 4 Ang. of Mon
B.

Steve



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Xiaoyi Deng
Sent: Thursday, September 20, 2007 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to calculate the contacts between the dimer- 
dimer

interface

Dear all:

I used moleman2 to calculate the contacts between chain A and B. Can
anyone suggest a program to calculate the contacts between the  
interface


of dimer-dimer?

Thank you,

Xiaoyi

Graduate student
University of Nebraska Medical center




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