[ccp4bb] Pisa application

[Careina Edgooms]

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be used/modified 
to detect potential interfaces of interaction of different proteins? This would 
be very useful as a tool to validate protein-protein interactions detected by 
in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, 
does anyone know of other software that could do a similar thing?

Best
Careina 

Re: [ccp4bb] refining large region with multiple conformers

[Lijun Liu]

Hi,

~1/3 of a chain that show substantial difference suggests a  
possibility that may deserve a check---the symmetry is actually lower  
and the 2 conformations belong to two occ=1 mols (unless the SG is  
already P1).


I had a case that the apo SG was P1 and ligand-bound (soaked) SG was  
P1 too but the binding made the data very well reducible to P2.  When  
refined with P2, I got something like you mentioned.  When going back  
with P1, everything turned to be clean, also R and Rfree were ~3% lower.



Lijun



On Aug 7, 2012, at 9:59 AM, Kendall Nettles wrote:


Hi,
We have a structure with the ligand showing two overlapping  
conformers. When we refine it with both conformers separately, it is  
pretty clear that there are substantial differences in the protein  
as a result, for about a third of the protein chain. My question is,  
would it be better to try to define alternate conformers for those  
specific regions, or would it be OK to refine with two entire  
alternate protein chains? There is also a second protein chain that  
shows only a single binding mode for the ligand.  It's a 2.0  
angstrom structure. The yellow 2Fo-Fc map goes with the green model  
in the attached pic. Also, do we want to let each amino acid have  
its own occupancy? or should one ligand copy and one chain all have  
the same occupancy? I'm leaning towards the latter since the  
differences should be directly tied to the ligand binding mode.

Kendall Nettles

Re: [ccp4bb] balbes solution

[Greg Costakes]

Hi Faisal, 


The solutions from BALBES have already gone through multiple rounds of 
refinement which minimize the R/Rfree. If you make a number of drastic changes 
to side chains or add waters, the R/Rfree should go down. However if the 
structure fits the density well (with no side chains needing major adjustment) 
and you have not yet added waters... you will not notice the R/Rfree go down. 


What are you R/Rfree values? 

--- 
Greg Costakes 
PhD Candidate 
Department of Structural Biology 
Purdue University 
Hockmeyer Hall, Room 320 
240 S. Martin Jischke Drive, West Lafayette, IN 47907 


 
** Hard work often pays of in time, but Procrastination always pays off now ** 

- Original Message -
From: "Faisal Tarique"  
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Tuesday, August 7, 2012 4:40:38 PM 
Subject: [ccp4bb] balbes solution 



Dear all 


i submitted one job in BALBES at YSBL server. The final outcome are showing the 
result to be definite solution by stating it to be a 99%solution. but when i am 
refining with refmac, Rwork and Rfree is not coming down despite my several 
tries. In COOT i can see tye missing density for loop region. the data is of 
2.5 angstrom resolution. -- 
Regards 

Faisal 
School of Life Sciences 
JNU 

[ccp4bb] balbes solution

[Faisal Tarique]

Dear all

i submitted one job in BALBES at YSBL server.  The final outcome are
showing the result to be definite solution by stating it to be a
99%solution. but when i am refining with refmac, Rwork and Rfree is not
coming down despite my several tries.  In COOT i can see tye missing
density for loop region.   the data is of 2.5 angstrom resolution.
-- 
Regards

Faisal
School of Life Sciences
JNU

Re: [ccp4bb] refining large region with multiple conformers

[Dale Tronrud]

   You have to build the model you actually believe matches what is in
the crystal.  Do you believe that each amino acid is occupying two
conformations independent of its neighbors?  I wouldn't go that way.
I would start with an apo conformation, labeled with 'g', and a holo
conformation including the ligand, labeled with 'h', and allow all of
'g's one occupancy value, and the 'h's another, and insist that they
sum to 1.0.  You may have to build water molecules in the binding site
of 'g' that are displaced by the ligand in 'h'.

   If this, simplest of models, doesn't do the trick you have to be
lead by your difference maps and chemical intuition to devise more
complex models.  Select the simplest model that makes sense and fits
your data.

   It would be interesting to see if you can find a program that would
allow you to restrain the ncs of the second protein chain and the 'h'
conformation of your mixed model, leaving the 'g' conformation unrestrained
by ncs.

Dale Tronrud

P.S. I'm avoiding the use of 'A' and 'B' alt locs because these are
routinely used when splitting side chains but are almost never intended
to imply that all 'A's are coordinated with each other and all 'B's are
likewise.  To be proper, the reuse of alt loc codes for unrelated
conformations should not be allowed, but there are simply not enough
letters to allow the rule to be enforced.

On 08/07/12 07:59, Kendall Nettles wrote:
> Hi,
> We have a structure with the ligand showing two overlapping conformers.
> When we refine it with both conformers separately, it is pretty clear
> that there are substantial differences in the protein as a result, for
> about a third of the protein chain. My question is, would it be better
> to try to define alternate conformers for those specific regions, or
> would it be OK to refine with two entire alternate protein chains? There
> is also a second protein chain that shows only a single binding mode for
> the ligand.  It's a 2.0 angstrom structure. The yellow 2Fo-Fc map goes
> with the green model in the attached pic. Also, do we want to let each
> amino acid have its own occupancy? or should one ligand copy and one
> chain all have the same occupancy? I'm leaning towards the latter since
> the differences should be directly tied to the ligand binding mode. 
> Kendall Nettles

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[Peter Goettig]

Dear David,

As suggested I have reinstalled Windows CCP4 6.2.0, but the problem of the 
missing information in the SCALA summary table was not abolished. In fact, it 
occurred in AIMLESS as well! I had done the original data processing in iMOSFLM 
1.0.7, followed by  a run of REINDEX to set the space group to P21212 with c as 
shortest axis including a reflection transformation.

Thus, I installed the Linux CCP4 6.3.0 and used the previous reindexed.mtz in 
SCALA. Everything worked perfectly and I obtained the desired tables with full 
information.

Regards,

Peter

Re: [ccp4bb] dumb software question

[Joel Sussman]

7-Aug-2012 20:30
Dear Paul,
Pls see "Virtual nanoscopy: Like 'Google Earth' for cell biologists"
http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615&et_rid=54732139&linkid=http%3a%2f%2fwww.rdmag.com%2fNews%2f2012%2f08%2fLife-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists%2f
Is this what you were looking for?
best regards,
Joel

On 7 Aug 2012, at 18:24, Paul Kraft wrote:


Hi guys,
is there a program similar to ccp4/coot that allows one to visuallize an ideal 
cell (either prokaryote or eukaryote) in 3D with semi accurate distances. One 
that is windows based (as much as I detest) that would be good for teaching 
biochem 380 students emphasising distance, diffusion, etc measurements with 
links to the pdb? Thanks in advance.
Paul

Dr. Paul Kraft
Structural Biologist
cell 586-596-2770
email: haresea...@yahoo.com

Re: [ccp4bb] dumb software question

[Jacob Keller]

You mean "cell" in terms of a living cell, not a unit cell, right?

JPK

On Tue, Aug 7, 2012 at 10:24 AM, Paul Kraft  wrote:

>
> Hi guys,
> is there a program similar to ccp4/coot that allows one to visuallize an
> ideal cell (either prokaryote or eukaryote) in 3D with semi accurate
> distances. One that is windows based (as much as I detest) that would be
> good for teaching biochem 380 students emphasising distance, diffusion, etc
> measurements with links to the pdb? Thanks in advance.
> Paul
>
> Dr. Paul Kraft
> Structural Biologist
> cell 586-596-2770
> email: haresea...@yahoo.com
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] dumb software question

[Bosch, Juergen]

http://www.cgl.ucsf.edu/chimera/ ?

Jürgen

On Aug 7, 2012, at 11:24 AM, Paul Kraft wrote:


Hi guys,
is there a program similar to ccp4/coot that allows one to visuallize an ideal 
cell (either prokaryote or eukaryote) in 3D with semi accurate distances. One 
that is windows based (as much as I detest) that would be good for teaching 
biochem 380 students emphasising distance, diffusion, etc measurements with 
links to the pdb? Thanks in advance.
Paul

Dr. Paul Kraft
Structural Biologist
cell 586-596-2770
email: haresea...@yahoo.com

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

[ccp4bb] dumb software question

[Paul Kraft]

Hi guys,
is there a program similar to ccp4/coot that allows one to visuallize an ideal 
cell (either prokaryote or eukaryote) in 3D with semi accurate distances. One 
that is windows based (as much as I detest) that would be good for teaching 
biochem 380 students emphasising distance, diffusion, etc measurements with 
links to the pdb? Thanks in advance.
Paul


Dr. Paul Kraft
Structural Biologist
cell 586-596-2770
email: haresea...@yahoo.com

[ccp4bb] joint EMBL-CCP4 training course in macromolecular crystallography

[Victor Lamzin]

We would like to announce a joint EMBL-CCP4 training course "European 
School for Macromolecular Crystallography (ESMAX)", which will build 
upon the traditions of the forefront of training in structural biology – 
the M2M workshops and the CCP4 crystallography schools. The first 
ESMAX-2012 course will take place at the EMBL Hamburg Outstation, the 
DESY synchrotron site during the period:


Monday November 19th to Monday November 26th, 2012.

The ESMAX-2012 course will include a range of activities addressing 
essential steps in determining biomolecular structures. In particular, 
the courses will have practicals on the use of synchrotron radiation and 
beamline equipment, sample handling and carrying out an experiment, 
followed by an intense course on data processing, structure solution, 
model building and validation using top-ranked software packages.


Speakers and tutors include G. Bourenkov (Hamburg), C. Carolan 
(Hamburg), M. Cianci (Hamburg), Z. Dauter (Argonne), K. Diederichs 
(Konstanz), W. Kabsch (Heidelberg), J. Kallio (Hamburg), R. Keegan 
(Didcot), E. Krissinel (Didcot), V. Lamzin (Hamburg), A. Lebedev 
(Didcot), B. Lohkamp (Stockholm), W. Minor (Charlottesville), G. 
Murshudov (Cambridge), S. Panjikar (Melbourne), N. Pannu (Leiden), H. 
Powell (Cambridge), T. Schneider (Hamburg), T. Schwede (Basel), T. 
Wiegels (Hamburg).


The number of places is restricted to 20. Applications can be made 
electronically via the link 
http://www.embl-hamburg.de/training/events/2012/ESMAX-12/index.html


The deadline for applications is October 1st, 2012.

The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan, 
Eugene Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider

Re: [ccp4bb] not strictly crystallography-related (summary)

[Kay Diederichs]

Dear all,

thanks for the many answers sent privately or posted to CCP4BB! I cannot answer 
them all individually, and I also cannot answer the questions that some people 
asked, since I have not yet heard back from my colleague whose experiment that 
is. But I'm sure there are some options for him, which I summarize below:

a) nanodiscs -see http://en.wikipedia.org/wiki/Nanodisc
b) DNA helicases oligomerize and look like a doughnut- not sure if that meets 
the disk-like shape, but if it does, there is a company called biohelix that 
will provide their helicases to the research community (not commercially 
available, but if you contact them and tell them you are doing research 
(biophysical experiment) and would like some protein, they will send you some. 
They use the helicases in making their products, but it's not the product they 
sell; however, they will provide some for research experiments. Here's the link 
- http://www.biohelix.com/products/helicases_customorder.asp
c) I do not know if it is strictly what you are after but you may want to 
investigate Beta-propeller folds which are disk-like. Lots of lectins are Beta 
propellers. You may want to look at Sigma lectins and check which ones are 
beta-propellers.
d) 2-cys peroxiredoxin might do the trick. i don't know if it's commercially 
availabe though...
e) The chaperonin 10 from groes is a heptamer that could be described as a disk 
shape. It is available from Sigma (C7438) at a cost of £285 per 0.25mg, but you 
may get a discount on a bulk order.
f) Hemopexin tetramer 
(http://www.sigmaaldrich.com/catalog/product/sigma/H9291?lang=es®ion=ES).
g) hexameric CcmK4 (http://www.sciencemag.org/content/309/5736/936.full) and 
cysteine-crosslinked HIV-1 CA hexamer 
(http://www.ncbi.nlm.nih.gov/pubmed/19523676). Neither is commercially 
available, but the plasmids are available from the authors and express to ~50 
mg/L in E.coli.
h) I guess the insulin hexamer is pretty disk like? And it is cheap and easy to 
crystallise..

thanks again to all who responded!

Kay

Re: [ccp4bb] column profile

[Edwin Pozharski]

Note that gel filtration columns need to be calibrated separately for 
different buffer.  S100 is a preparative column not quite intended for 
molecular weight determination, but if that is what you are doing, it's 
important to do your own calibration.


On 08/07/2012 03:20 AM, MT wrote:

Have a look at this pdf.

Regards.

https://www.gelifesciences.com/gehcls_images/GELS/Related%20Content/Files/1314750913712/litdoc28407384AA_20110831032125.pdf


Le 6 août 2012 à 10:23, sajid akthar  a écrit :


Hi all

If anyone have, please post the calibration profile for GE Sephacryl S100 26/60 
Hiprep column. Sorry I could not locate in the GE Healthcare site.

Thankx in advance

Sajid

[ccp4bb] BBSRC-CASE PhD studentship (UK residents only)

[Mayans, Olga]

Dear colleagues, 

The position below does not strictly relate to structural biology, but it 
involves a good amount of protein engineering and biophysical analysis. 
Candidates with a background in protein biochemistry are particularly welcome 
to apply. 


-- 4 Year BBSRC CASE PhD Studentship --

**(UK RESIDENTS ONLY)**

Title: Development of engineered proteins that can assist the differentiation 
of hyaline chondrocytes from mesenchymal stem cells

(Available to start from 1st October 2012 or as soon as possible thereafter) 

Osteoarthritis (OA) is a degenerative joint disease caused by loss of hyaline 
chondrocytes. Mesenchymal stem cells (MSC) can readily differentiate to 
chondrocytes in vitro, and are thus a promising source for OA cell therapy. 
Recent research performed in the laboratory of the lead supervisor, Patricia 
Murray, has shown that novel biomimetic substrates can induce the 
differentiation of MSC to chondrocytes, without the need for additional growth 
factors. Building on those findings, a major aim of this project is to use new 
engineered proteins developed in the laboratory of the co-supervisor, Olga 
Mayans, to fabricate biomaterial scaffolds capable of maintaining the phenotype 
of MSC-derived hyaline chondrocytes. In this, we will work closely with the 
CASE Partner, Joint Replacement Instrumentation Ltd (JRI), to implement 
commercialisation strategies for any novel culture conditions, media 
compositions and engineered biomaterials arising from the project.

This project is particularly suited to individuals with an interest in the 
engineering of biomolecular systems for cellular applications. The appointed 
researcher will be trained in techniques such recombinant protein production 
and protein engineering, MSC culture and differentiation, quantitative 
real-time PCR, immunostaining and confocal microscopy. The student will also 
gain awareness of working in a commercial environment. 

The candidate should have obtained a good BSc degree and/or a Master’s degree 
in biochemistry, molecular biology or a related area. Basic familiarity with 
the production of proteins or the handling of cells will be of advantage.

A motivation letter and CV should be sent to patricia.mur...@liv.ac.uk. 


Dept/School:  Institutes of Translational Medicine and Integrative Biology, 
University of Liverpool
Academic Supervisors:   Dr Patricia Murray (p.a.mur...@liv.ac.uk)
Dr Olga Mayans (may...@liv.ac.uk)
Industrial SupervisorsDr Anita Czenkusz (anita.czenk...@jri-ltd.co.uk) 
Dr Edward Draper 
(edward.dra...@jri-ltd.co.uk)
Funding Availability: FullyFunded PhD project (UK Students Only)

[ccp4bb] Knauer Bioline chromatography system

Dear all,

Has anyone used the Knauer bioline chromatography system?

Can you please share your experience?

Thanks in advance

Regards

Subhash C Bihani

[ccp4bb] Postdoc positions in X-ray crystallography or electron microscopy at Imperial College London

[Zhang, Xiaodong]

Research Associate: London, United Kingdom
Imperial College London

Salary: £32,100 - £40,720 per annum
We are seeking two Research Associates to work in the research group of 
Professor Xiaodong Zhang (www.msf.bio.ac.uk) in the 
Centre for Structural Biology, at the South Kensington Campus of Imperial 
College London. Funded by a Wellcome Trust Senior Investigator Award to 
Xiaodong Zhang, you will join a group of multi-disciplinary colleagues and 
collaborators to investigate the structures and mechanisms of DNA damage 
response.
These fixed-term posts are available for up to five years.
You must hold a PhD in a structural biology or biochemistry discipline or a 
related discipline, or an equivalent level of professional qualifications and 
experience. Research experience in a structural biological laboratory 
environment (covering either X-ray crystallography, or electron microscopy 
single particle analysis), and knowledge of protein biochemistry are essential.
For informal enquiries please contact Professor Xiaodong Zhang 
xiaodong.zh...@imperial.ac.uk.
Our preferred method of application is online via our website 
http://www3.imperial.ac.uk/employment (please select “Job Search” then enter 
the job title or vacancy reference – NS 2012 163 IL - number including spaces 
into “Keywords”).  Please complete and upload an application form as directed.
Closing Date: 4 September 2012 (Midnight BST)



Professor Xiaodong Zhang
Imperial College London
Division of Molecular Biosciences
504, Wolfson laboratories
South Kensington, London, SW7 2AZ
(0) 207 594 3151
xiaodong.zh...@imperial.ac.uk
http://www.imperial.ac.uk/people/xiaodong.zhang

Re: [ccp4bb] column profile

[MT]

Have a look at this pdf.

Regards.

https://www.gelifesciences.com/gehcls_images/GELS/Related%20Content/Files/1314750913712/litdoc28407384AA_20110831032125.pdf


Le 6 août 2012 à 10:23, sajid akthar  a écrit :

> Hi all
> 
> If anyone have, please post the calibration profile for GE Sephacryl S100 
> 26/60 Hiprep column. Sorry I could not locate in the GE Healthcare site.
> 
> Thankx in advance
> 
> Sajid