[ccp4bb] Reference for hanging drop crystallization

[Shane Caldwell]

Hi ccp4bb,

I've been asked to provide a reference for making hanging-drop crystals,
and I suppose that I never realized the need to cite the technique
specifically. Is there a definitive publication where one could trace the
origins of the technique, or a particularly thorough textbook or review?

Shane Caldwell
shane.caldwel...@gmail.com

[ccp4bb] ccp4 release 7.0 update 053

[Charles Ballard]

Dear All

a further update to the series 7.0 ccp4 release containing

* refmac5 - bug fixes and speedup

* crank2 - bug fixes

* arcimboldo

* morda

* fragon (linux and osx)

* buccaneer

* nautilus

* ccp4mg

All the best

Charles

ps - next update to contain shelxe and a monomer library update

Re: [ccp4bb] Looking at an EM map..

[Garib Murshudov]

Yes. that is how it should be done. if you have a map then you convert them to 
Fourier coefficients directly using Fourier transformation.

Only for some particles density maps are positive everywhere. X-ray particles 
are one of them.
For neutron and electron scattering maps could be negative as well as positive.

For electron diffraction in a simplified form there is a relationship (and it 
is used in some programs, including refmac) between X-ray and electron 
scattering factors. Using the fact that electron density and electrostatic 
potential are related by Poisson equation Mott-Bethe derived a formula:

f_e(s) PropTo  (Z-f_X(s))/s^2

Z is nuclear charge and f_x(s) is X-ray form factor (Fourier transformation of 
spherical form of electron density of an atom. f_x(0) is the total number of 
electrons. For charged atoms at s=0 Z-f_X(s) is different from 0 and therefore 
for positively charged atoms it could be very large positive number. and for 
negatively charged atom it could be very negative number. (There is screening 
effect related to realignment of charges around charges also, but still 
negatively charged atoms will have negative scattering factors at low 
resolution). At higher resolution all scattering factors become positive. So, 
if you measurement (density) is at low resolution then density map can be 
negative. It is true for EM as well as electron diffraction.

There is an additional complications in EM when you compare maps from 
reconstruction to the atomic electrostatic potential: maps have been subjected 
to some filtering procedure. 

An additional complication in density maps after scattering experiment is that 
scattered particles can knock out some hydrogens (eventually knocking out some 
of atoms or group of atoms) and the result could be an accumulation of negative 
charges and therefore (at low resolution) weakening of maps, in some cases 
making them negative. There are few more complications  (direction dependence, 
solvent behaviour, dynamic scattering effects etc).

Regards
Garib
 P.S. I am sorry that this mail turned out to be longer than I wanted.




On 15 Mar 2018, at 14:41, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> So if I calculate "structure factors" from a map do I just use the map as is 
> with the negative values included ?
> 
> Eleanor
> 
> On 15 March 2018 at 14:37, Ian Tickle  wrote:
> 
> Hi Eleanor
> 
> Electron scattering factors can be negative for negative ions, particularly 
> at low d*.  For a low-resolution map it means that the electric potential is 
> the opposite sign to what you expected.  It's why you often don't see ASP & 
> GLU side-chains in low resolution EM maps.
> 
> Cheers
> 
> -- Ian
> 
> On 15 March 2018 at 14:17, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> I am pig-ignorant about these ,, but this example has negative values as well 
> as positive.. 
> 
> What does this mean? I thought a well phased map would be pretty well all 
> positive..
> 
>  Eleanor
> 
> 

Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge 
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk, 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

[ccp4bb] Subject: CCP-EM Icknield Workshop for High Resolution Model Building and Refinement - Registration Open

[Tom Burnley]

Dear all,

We are proud to announce the 2018 Icknield Workshop kindly supported by
Instruct. This course is aimed at structural biologists with high
resolution EM maps ready for / in the process of model building and
refinement. This four day course (1st-4th May) will host some of the
leading software developers and provide ample contact time to allow
delegates to discuss their data in detail alongside traditional lectures
and tutorials. It will cover all aspects of model building including: map
optimisation, docking, automated model building, medium resolution
refinement, high resolution refinement, interactive refinement, validation
and deposition.

The course will be held at the RAL / Diamond Campus, Harwell, UK, site of
the eBIC national facility. Registration is free, thanks to generous
funding from Instruct, and we will provide food and three nights
accommodation at the Bear Hotel in nearby Wantage (nights of 1st, 2nd and
3rd May). Please note that during the application process you will be asked
if you would like to make an accommodation request - if you would like
accommodation provided for you free of charge please select yes and let us
know which nights you would like. If you do not want accommodation provided
for you please select no. Delegates are asked to meet their own travel
costs. Please see the agenda for full course times.

The course is limited to 20 delegates who will be selected from all
applicants.  A maximum of 50 applicants can register interest.

Applications will close on ***Wednesday 28th March*** and the 20 successful
applicants will be informed the following day. Please note the short
registration time as we would like to strongly encourage applicants to work
on 'live' datasets.

* Registration site:
cvent.com/d/btq6g6

* Confirmed tutors / topics:

Tristan Croll (Cambridge)
ISOLDE: Interactive model building/real-space refinement based on
interactive molecular dynamics

Kevin Cowtan (York)
Buccaneer: automated model building

Paul Emsley (MRC-LMB Cambridge)
Coot: macromolecular model building, model completion and validation

Arjen Jakobi (Delft)
LocScale: scaling tool using prior model information to improve map
contrast

Oleg Kovalevskiy (Murshudov group, MRC-LMB Cambridge)
Refmac: refinement of high-resolution EM structures

Ardan Patwardhan (EBI)
EMBD: deposition in EMBD

Joerg Schaarschmidt (Bonvin Group, Utrecht)
Powerfit: Fast and sensitive rigid-body fitting into cryo-EM density maps

Maya Topf (Birkbeck)
FlexEM: fitting and refinement of atomic structures guided by cryoEM density


Best wishes,

Tom and the CCP-EM team


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em * | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871