[ccp4bb] Advice on Enzyme Kinetics (substrate bound plate format)

[Stephen Connelly]

I am looking for some expert advice on enzyme kinetics but for an assay in 
plate format which has the substrate bound. This is different that the usual 
homogeneous plate assays or heterogeneous assays where the enzyme (catalyst) is 
plate bound. 

In short I am trying to look at the Ki of a compound and wish to use a plate 
assay as the compound absorbs at the same wavelength as the typical 
para-nitroanaline substrate that is usually used.

Is it possible to do normal Michaelis Menten kinetics in a plate format given 
the substrate is bound and not homogeneous despite rigorous shaking? 

We believe the inhibitor is mixed in its mechanism, it binds non covalently but 
does seem to react, albeit poorly with the Cys nucleophile in the protease. We 
have shown this through a few different studies but wish to obtain a Ki and 
generate a graph that will provide evidence of either competitive or mixed 
inhibition.

Hoping to hear form you all!!!

Thanks - Steve - Email:conne...@scripps.edu

[ccp4bb] Position in Structural Biology of Nucleic Acids/Protein Complex

[Dong Wang]

An immediate opening for a protein crystallographer position in UC San Diego. 
The research is focused on the structural and functional investigation of 
Nucleic Acids/Protein complexes.

The successful candidate should have a fresh Ph.D. in structural biology in 
nucleic acids/protein complex and at least two first author papers in this 
area. The candidate shall expected to have extensive experiences in determining 
crystal structures and have experience in molecular biology and protein 
biochemistry. 

Interested candidates can email a CV, three contacts for reference to Dr. Dong 
Wang at dongw...@ucsd.edu.
For more information regarding the Wang Laboratory, please see the website:  
http://pharmacy.ucsd.edu/labs/wang/

[ccp4bb] Monomer Library Sketcher

[Huiying Li]

Another problem we encountered with the newly installed CCP4 6.3.0 on a 
64-bit Linux computer:


The graphic window of Monomer Library Sketcher can't pop up, giving the 
following error:

Can not run Monomer Library Sketcher with the BLT extension to Tcl/Tk
installed. See your system manager or the CCP4i installation
documentation

Appreciate any help to fix the problem.

Regards,
Huiying
-
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
email: h...@uci.edu

[ccp4bb] Position in structural immunology

[Steve Almo]

A position is immediately available in the structural immunology program at the 
Albert Einstein College of Medicine to pursue the expression, purification and 
structure determination of a wide range of immune modulatory proteins and 
complexes. Familiarity with high resolution structure determination is 
desirable, but documented expertise in eukaryotic expression and bacterial 
inclusion body technologies is essential. These efforts are part of the New 
York Structural Genomics Research Consortium, which is supported by 
state-of-the-art infrastructure for both bacterial and eukaryotic expression, 
including extensive automated liquid handling and tissue culture robotics 
within a BSL2 environment. Interested candidates should forward a CV and the 
names of at least two references to:
Steve Almo (steve.almo [at] einstein.yu.edu).

[ccp4bb]

[Runjhun Saran]

Dear All,

Thanks a lot for the help, PISA and CCP4 has really helped me a lot!

Regards,
Runjhun

On Fri, Aug 10, 2012 at 9:11 PM, Jawahar Sudhamsu wrote:

> Hi Runjhun,
>
> This server works well for calculating inter-molecular protein
> interactions.
>
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
>
> you could also you pymol and get interacting surfaces by selecting for
> residues with 4.0 A of chain A and chain B for example.
>
>
> Hope this helps.
>
> Sudhamsu
>
>
> On Fri, Aug 10, 2012 at 7:44 AM, Runjhun Saran wrote:
>
>> Hello everyone..
>>
>> This is Runjhun Saran. I am new to studying inter-molecular protein
>> interactions and the residues involved in them. Can anyone suggest me
>> online websites or freely available softwares where we can put in the PDB
>> files of the interacting molecules and get the residues involved in their
>> interaction?
>>
>> Thanking you,
>>
>> Regards,
>> Runjhun
>>
>>
>>
>

[ccp4bb] Symposium in Membrane Protein Crystallisation - UK

[Dr. Isabel De Moraes]

Dear All,

The Membrane Protein Laboratory (MPL) at Diamond Light Source is organising a 
Symposium in Membrane Protein Crystallisation on the 27th of September at the 
Research Complex at Harwell - UK

The registration is now open:
http://www.rc-harwell.ac.uk/symposium-in-membrane-protein-crystallization

There are a maximum of 75 places and the registration will be closed once all 
the places are taken.
Program
Symposium in Membrane Protein Crystallization
9:45 - 10:15arrival/registration
10:15 - 10:30   welcome
Session 1   Chair: Prof. Steve Mathews - Imperial College London
10:30 -11:00Introduction to Membrane Protein Crystallization
Isabel Moraes - Diamond - MPL
11:00 -11:30Stabilising Membrane Protein Samples for Crystallization
Paul Thaw and Jeanette Hobbs - Molecular Dimensions
11:30 - 12:00   lipidic Cubic Phase Technologies for Membrane Protein 
Structural Studies
Vadim Cherezov - The Scripps Research Institute - USA
12:00 - 12:30   Membrane Protein Nano and Macro Crystallization using Lipidic 
Sponge Phases
Linda Johansson - University of Gothenburg - Sweden
12:30 - 13:30   lunch
Session 2   Chair: Prof. Thomas Sorensen - Diamond Light Source
13:30 - 14:00   The Use of Bicelles in Membrane Protein Crystallization
Jeff Abramson - University of California, Los Angeles - USA
14:00 - 14:30   Current Trends in Alpha Helical Membrane Protein 
crystallization - The Rationale Behind MemGold, MemGold2 and MemAdvantage 
Screens
Simon Newstead - University of Oxford
14:30 - 15:00   Advances in Automated Imaging and Liquid Handling to Support 
Membrane Protein Research
Olivia Sleator - Rigaku
15:00 - 15:30   Crystallizing GPCRs for Drug Discovery
João Dias - Heptares
15:30 - 16:00   Break
session 3   Chair: Dr Alex Cameron - Imperial College London
16:00 - 16:30   Imaging Protein Crystals with Ultrafast Lasers
Ellen Gualtieri - Formulatrix
16:30 - 17:00   Exploiting Microfocused X-rays for Challenging Problems in MX
Robin Owen - Diamond Light Source
17:00 - 17:30   BLEND - The systematic Scaling and Merging of Multiple Datasets 
in Macromolecular crystallography
James Foadi - Diamond - MPL
17:30   Closing remarks



Sponsors
 
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We would be delighted to meet you at the symposium.


With best Regards,
Isabel Moraes

-
Dr. Isabel De Moraes, MRSC

Membrane Protein Laboratory Facility Co-ordinator
Membrane Protein Laboratory
Diamond Light Source Ltd,
Chilton, Didcot, Oxfordshire,
OX11 ODE, UK

Tel (direct): 01235 778664
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Re: [ccp4bb] Various OSes and Crystallography

[William G. Scott]

I completely agree with Harry's observation about the glare screen "feature."  
I find it is quite literally an almost instant headache.  There is an option 
with the macbook pro to pay a ransom to get a usable screen, so my wife did.  
On my macbook air, I found putting a dull dark grey background for a desktop 
helps considerably to cut down on the reflection, perhaps in part because it 
reflects my personality.  Instead of buying iMacs, we now get mac minis and 
pair them with Samsung LED matte screen monitors.  The improvement is 
considerable, and they are a lot less expensive too.


Bill


On Aug 9, 2012, at 11:25 PM, Harry  wrote:

> Hi
> 
> My two ha'porth.
> 
> For  a laptop, this is the clincher for me - if you want to use your laptop 
> anywhere that has reasonable light levels (e.g. demonstrating to anyone in an 
> exhibition hall), you may well find that the beautiful shiny mirror that 
> Apple put on the front of their screens on most of their laptops makes your 
> investment almost useless in reasonable levels of ambient light. Unless I 
> could buy a Macbook with a matt screen I doubt I'd want to buy another one.
> 
> Sometimes I wonder if my Macbook was "designed in California in a cave" to 
> paraphrase what it says on the sticker on the back...
> 
> It runs all the software I want it to without problems, though, including 
> WIndows stuff via wine or VMWare. And I do *really* like OSX as an interface.
> 
> On 9 Aug 2012, at 16:18, Andreas Förster wrote:
>> 
>> Mind that if you buy a MacBook, there's only one (hefty 15") model without a 
>> mirror-coated screen.
>> 
>> 
>> Andreas
>> 
>> 
>> 
>> On 09/08/2012 3:58, Nat Echols wrote:
>>> On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
>>>  wrote:
 one. Are there any really reasonable arguments for preferring Mac over
 windows (or linux) with regard to crystallography? What can Mac/Linux do
 that windows cannot (especially considering that there is Cygwin)? What
 wonderful features am I missing?
>>> 
>>> Mac vs. Linux: mostly a matter of personal preference, but I agree
>>> with Graeme.  Most programs run equally well on either - with Coot a
>>> partial exception, apparently due to problems with the X11
>>> implementation (but once you get used to these, it's not a big deal).
>>> 
>>> Windows, on the other hand, simply doesn't support the full range of
>>> modern crystallography software.  And in my experience, it has
>>> crippling flaws that mean some programs will always work better on
>>> Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
>>> scientific computing unless you need to run an application that won't
>>> work on any other OS, and as far as I know there isn't a single
>>> (macromolecular) crystallography program that falls into this
>>> category.
>>> 
>>> -Nat
>>> 
> 
> Harry
> --
> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
> Cambridge, CB2 0QH

[ccp4bb]

[Bosch, Juergen]

one interpretation of your question could be answered with
CCP4i using Contact http://www.ccp4.ac.uk/html/contact.html and listing 
contacts between say chain A and B.
You can do this also with the PISA server, assuming your PDB contains the 
proteins in question as a complex.
Manually you could pursue the question with Coot or Pymol and a piece of paper 
and pencil
If your proteins have not been co-crystallized, you could try protein-protein 
docking.
It would help if you specified your question a bit more.

Jürgen


On Aug 10, 2012, at 10:44 AM, Runjhun Saran wrote:

Hello everyone..

This is Runjhun Saran. I am new to studying inter-molecular protein 
interactions and the residues involved in them. Can anyone suggest me online 
websites or freely available softwares where we can put in the PDB files of the 
interacting molecules and get the residues involved in their interaction?

Thanking you,

Regards,
Runjhun



..
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] having difficulties with ammonium ion

[Afshan Begum]

Hello all, 

I am refining  my structures with REFMAC 5 and is failed. Actually i used 
ammonium dihydrogen phosphate buffer during crystallization and in the map file 
where i observed the density of ammonium ion (NH4). I get this ion from the 
coot library but when i run refmac its failed even i gave the cif file for this 
ion as a supplement but i could not get success so, if any body give me 
suggestion how to solve this problem.

I would be thankful to all.

this are the error message came from refmac log file



 ERROR : atom :H4_N NH4 1  FF   is absent in the library
  ATTENTION: atom:N    NH4 1  FF   is missing in the structure
  ERROR : atom :H4_N NH4 2  Fa   is absent in the library
  ATTENTION: atom:N    NH4 2  Fa   is missing in the structure
  ERROR : atom :H4_N NH4 3  Fb   is absent in the library
  ATTENTION: atom:N    NH4 3  Fb   is missing in the structure
  ERROR : atom :H4_N NH4 4  Fc   is absent in the library
  ATTENTION: atom:N    NH4 4  Fc   is missing in the structure
  ERROR : atom :H4_N NH4 5  Fd   is absent in the library
  ATTENTION: atom:N    NH4 5  Fd   is missing in the structure
  ERROR : atom :H4_N NH4 6  Fe   is absent in the library
  ATTENTION: atom:N    NH4 6  Fe   is missing in the structure
  ERROR : atom :H4_N NH4 7  Ff   is absent in the library
  ATTENTION: atom:N    NH4 7  Ff   is missing in the structure

Best Regards

AFSHAN

[ccp4bb]

[Runjhun Saran]

Hello everyone..

This is Runjhun Saran. I am new to studying inter-molecular protein
interactions and the residues involved in them. Can anyone suggest me
online websites or freely available softwares where we can put in the PDB
files of the interacting molecules and get the residues involved in their
interaction?

Thanking you,

Regards,
Runjhun

[ccp4bb] UEFI Secure Boot ( was Re: [ccp4bb] Various OSes and Crystallography)

[Peter Keller]

Dear all,

This discussion about OS's seems like a good time to flag up the UEFI
Secure Boot issue, for any of you who haven't heard about it. Quite what
it means for Linux depends on whose commentary you read, but it is just
possible that the carefree days of buying any x86-based system with
standard hardware and installing whatever Linux distro you like on it
are coming to an end.

I don't pretend to grasp all the details, but if I have understood
correctly, the following scenario will become theoretically possible
when Windows 8 certified hardware goes on sale around October 26:

(1) You buy a Windows 8 certified machine with Windows 8 pre-installed.

(2) You attempt to install a Linux distro on it, like you have done in
the past with other hardware. This fails.

(3) You do a bit of research, work out that Secure Boot is likely to be
the problem, and that the particular Linux distro you want to install
won't work with Secure Boot at all.

(4) With a bit more reading, you find that Microsoft have specified as
part of the Windows 8 hardware certification requirements that disabling
Secure Boot should be possible for "a physically present user", at least
for x86-based hardware. [ARM-based hardware is another story, but that
is not of general interest to crystallographers.]

(5) The manufacturer of your new machine has decided that only 0.1%
of purchasers of their machines are going to want to disable Secure
Boot, so haven't bothered to actually implement and/or document a way of
doing it. They have also gambled that Microsoft aren't committed enough
to that part of their own requirements to take any action over its
violation (after all, they might say to themselves, it wouldn't make any
sense for Microsoft to withdraw Windows 8 certification from our
machines just because a few geeks can't install Linux on them).

I don't know how likely this scenario is, but disabling Secure Boot is
probably not a good thing to do if you want to use the machine to
dual-boot Windows 8 and Linux. If Secure Boot is a useful line of
defence against Windows malware, it would be better to leave it on and
have a way of booting into Linux without disabling it.

Some Linux distributors have taken various steps to cope with this issue
(or are at least thinking about it, with the expectation that they will
have figured out something in time), but it will be something to
consider when buying Windows 8 certified hardware in the future. It may
be a problem if you want to install a customised or non-mainstream Linux
distro. Also even if current/future Linux distro's implement ways of
working with Secure Boot, installing older versions may be problematic
(there are several reasons for wanting to use older OS's). I don't know
how using virtual machines will be impacted by this, if at all.

Please don't ask me for clarifications about all this. I am not an
expert and I am only paraphrasing what other people have written. If you
want to know more, these two links are reasonable starting points, and
are both reasonably up-to-date:





To my knowledge, RedHat/Fedora and Canonical (i.e. Ubuntu) have decided
on (different) solutions, both with some attendant controversy.
SUSE/openSUSE are actively working on it. I have not been able to find
anything about any plans by Debian. I also don't know what the impact
will be on RedHat derivatives like CentOS and Scientific Linux.

Regards,
Peter.

On Thu, 2012-08-09 at 08:55 -0500, Jacob Keller wrote:
> Dear List,
> 
> 
> I guess this is somewhat of a perennial issue, but I am faced with
> choosing an OS for a new computer, and am curious about benefits and
> drawbacks with regard to crystallography. So far, I have been using
> windows, and have found no limitations whatsoever, but then again,
> maybe I don't know what I am missing. But, since so many folks out
> there use Macs, I am open to using one. Are there any really
> reasonable arguments for preferring Mac over windows (or linux) with
> regard to crystallography? What can Mac/Linux do that windows cannot
> (especially considering that there is Cygwin)? What wonderful features
> am I missing?
> 
> 
> Jacob
> 
> 
> -- 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
> 

-- 
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom

Re: [ccp4bb] generating symmetry related

[Paul Emsley]

 On 10/08/12 08:05, anita p wrote:

Dear All,
I have a small molecule structure file coordinates in CSD CIF format,
I would like to analysis inter-molecular interaction between them by 
generating symmetry related nearest neighbor structures.
I want to store  the coordinates of the generated structures and 
further analysis it using in-house tools. Since i would like to do 
this for multiple structure, can anyone let me know of the a method or 
tool (command-line) without the use of GUI to get these structure.


You can do this with Coot (0.7-pre) if you can tolerate writing a bit of 
python script to loop over the number of symmetry operators for the 
save_symmetry_coords() function.


Paul.

Re: [ccp4bb] calculation of cavities within crystal protein

[Dr. Lorenzo Finci]

Danilo, There are two points that I want you to consider before I attempt to 
answer your question:1. In terms of capabilities:Voidoo has the capability to 
detect specific voids or all voids inside a bio-macromolecular complex, as well 
as certain cavities that are connected to the "outside world". It delineates 
these cavities, meaning that it finds  their extent in 3-dimensional space. 
Secondly, it measures the molecular volumes as well as the volume of the cavity 
itself. Finally, it has the capability to generate molecular surface plot files 
which enable the visualization of the cavities. Voidoo will detect voids and 
invaginations, but it cannot pick pockets, no pun intended :)2. In terms of 
measuring and displaying cavities, there are three particular modes:a. 
Vanderwaals cavity, where the cavity comprises the compliment of the 
Vanderwaals surface of the surrounding atoms.b. Probe-accessible cavity, where 
the cavity comprises all of the space that can be accessed by the center of the 
probe sphere.c. Probe-occupied cavity, where the cavity comprises all of the 
space that can be occupied by the probeNow to answer your question:The first 
step of the cavity detection algorithm is to map the target molecule onto a 
3-dimensional grid with a spacing (0.5 - 1 Angstrom). All of the grid points 
are initially assigned a value of zero. Every subsequent point of the grid 
whose distance to the nearest atom is less than the sum of the van der Waals 
radius of that atom and the probe radius, is assigned a value of 1. In order to 
exclude the outside world, all of the grid points on the faces of the grid are 
set to zero, and the outside world is "zapped".This method is also known as the 
"flood fill" algorithm. At the final stage, all grid points are inside a closed 
cavity and have a value of zero. Voidoo then checks if the cavity has been 
detected and will delineate the cavity to measure the volume. Then the process 
of "atomic flattening" is invoked, which entails multiplying the van der Waals 
radii of all atoms by a certain flattening factor. The program then goes 
through iterative rounds of atomic flattening to close off cavities which are 
in contact with the outside world, and separate cavities which are in contact 
with each other through small channels. The program will stop after the 
particular sought after cavity has been found. A detailed answer to your 
question can be found in the original resource that I sent in my first 
response:http://journals.iucr.org/d/issues/1994/02/00/gr0263/gr0263.pdfI hope 
this helps!lorenzoLorenzo Ihsan FInci, Ph.D.Postdoctoral Scientist, Wang 
LaboratoryHarvard Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking 
UniversityThe College of Life SciencesBeijing, China


> Date: Fri, 10 Aug 2012 10:39:29 +0200
> From: danilo.belv...@ic.cnr.it
> To: lfi...@hotmail.com
> Subject: RE: [ccp4bb] calculation of cavities within crystal protein
> 
>  Thanks you for your help Lorenzo.
>  VOIDOO seems to be the proper software for this calculation, and it is 
>  suggested by many people.
> 
>  I am not an expert in this field! So, I would have only one thing to 
>  ask, because of a doubt arising from what I read in 
>  http://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf.
> 
>  In the paper, VOIDOO is a "grid-based procedure that measures the 
>  cavity volume defined by the van der Waals surface of atoms lining the 
>  cavity"
>  Does this mean that van der Waals surfaces of a protein and the 
>  surrounding proteins are considered in the calculation?
> 
>  I hope not too disturbing you.
> 
>  Danilo
> 
>  On Thu, 9 Aug 2012 10:05:19 -0400, "Dr. Lorenzo Finci" 
>   wrote:
> > Danilo,
> >
> > The protein cavity can be analyzed utilizing the program Voidoo (
> > Kleywegt GJ, 1994). This program uses an atomic-flattening algorithm
> > based on a 3-dimensional grid to locate and delineate different
> > cavities. A Van Der Waals cavity can further be generated with a 
> > probe
> > radius with a computed cavity grid using the highest number of grid
> > points, and a contact and accessible surface can further be
> > evaluated...
> >
> > Relevant Resources:
> > 
> > http://pelican.rsvs.ulaval.ca/mediawiki/index.php/Analysing_protein_cavities_using_VOIDOO
> > http://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf
> >
> > I hope this helps!
> > lorenzo
> >
> > Lorenzo Ihsan FInci, Ph.D.
> > Postdoctoral Scientist, Wang Laboratory
> > Harvard Medical School
> > Dana-Farber Cancer Institute
> > Boston, MA
> > Peking University
> > The College of Life Sciences
> > Beijing, China
> >
> >> Date: Thu, 9 Aug 2012 13:53:09 +0200
> >> From: danilo.belv...@ic.cnr.it
> >> Subject: [ccp4bb] calculation of cavities within crystal protein
> >> To: CCP4BB@JISCMAIL.AC.UK
> >>
> >> Dear all,
> >>
> >> I am Dr. Danilo Belviso and I am working on a platinum-based
> > inhibitor
> >> for matrix-metallo proteasis.
> >>
> >> I have obtained the crystal structure of the adduct 

[ccp4bb] generating symmetry related

[anita p]

Dear All,
I have a small molecule structure file coordinates in CSD CIF format,
I would like to analysis inter-molecular interaction between them by
generating symmetry related nearest neighbor structures.
I want to store  the coordinates of the generated structures and
further analysis it using in-house tools. Since i would like to do this for
multiple structure, can anyone let me know of the a method or tool
(command-line) without the use of GUI to get these structure.

with regards
Anita