Re: [ccp4bb] ctruncate

[Kevin Cowtan]

There are two known issues with ctruncate: one with the anisotropic 
correction and one with the fitting of  as a function of resolution.


The first is easily addressed - try turning off the anisotropy 
correction. That may solve the problem.


Ricardo Aparicio wrote:

Dear all,

For the same input in a ccp4i (v .2.0.4) Scala (v. 3.3.9) job I have 
obtained the following:


with CTRUNCATE (v. 1.0.01)
==
Col SortMinMaxNum  % Mean Mean   Resolution   
Type Column
num order   Missing complete  abs.   Low
High   label


5 BOTH ?   ?  125860.00  ??  -999.00   0.00   F  
F_BA2


with TRUNCATE (v. 6.1)
==
5 NONE1.8   152.8   766   93.9120.2620.26  24.93   2.80   F  
F_BA2



The final file after Ctruncate cannot be read in by some programs 
although  mtzdump can dump it.


Thanks for any comments on possible reasons for this problem.

Ricardo

Re: [ccp4bb] write out unmerged Scalepack file in HKL2000

[Scott Walsh]

Hi Alexandra,

Sure.  Go to the Macros tab and add "no merge original index" during scaling 
window.

Cheers,

Scott

*
Scott T. R. Walsh, Ph.D.
Assistant Professor
Center for Advanced Research in Biotechnology
University of Maryland Biotechnology Institute
Rm 3127E CARB II
9600 Gudelsky Drive
Rockville, MD 20850
email: wal...@umbi.umd.edu
phone: (240) 314-6478
fax: (240) 314-6255
-- 

- Original Message -
From: Alexandra Deaconescu 
Date: Wednesday, September 9, 2009 8:50 pm
Subject: [ccp4bb] write out unmerged Scalepack file in HKL2000
To: CCP4BB@JISCMAIL.AC.UK

> Hi all:
> 
> Is there a way to write out UNMERGED Scalepack files from 
> HKL2000 ?  
> In the older days of Scalepack, I remember you could have a NO 
> MERGE  
> in the script, but what about the newer HKL2000?  If there 
> is a way ,  
> well, I could not find it...
> 
> Thanks  a lot,
> Alex
> 
> 
> Alexandra M. Deaconescu
> Postdoctoral Fellow
> Grigorieff Laboratory
> Brandeis University
> Rosenstiel Center MS 029
> 415 South St.
> Waltham, MA 02454
> USA
> 
> For deliveries:
> Brandeis University
> Kalman Dock
> 415 South St.
> Waltham, MA 02454
> USA
> 
> 
> 
>

[ccp4bb] write out unmerged Scalepack file in HKL2000

[Alexandra Deaconescu]

Hi all:

Is there a way to write out UNMERGED Scalepack files from HKL2000 ?  
In the older days of Scalepack, I remember you could have a NO MERGE  
in the script, but what about the newer HKL2000?  If there is a way ,  
well, I could not find it...


Thanks  a lot,
Alex


Alexandra M. Deaconescu
Postdoctoral Fellow
Grigorieff Laboratory
Brandeis University
Rosenstiel Center MS 029
415 South St.
Waltham, MA 02454
USA

For deliveries:
Brandeis University
Kalman Dock
415 South St.
Waltham, MA 02454
USA

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[Sean Seaver]

I say deposit it both ways, someone needs to start keeping those
computational chemists on their toes.

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[Jürgen Bosch]

P6122 or P6522 make sure you get it right, otherwise the  
SpaceGroupPolicePatrol will get you :-)


Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[Ezra Peisach]

William G. Scott wrote:


On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote:

If you want to gamble - go w/ P6122... Data from the PDB  indicates 
that there are 1.5x as many proteins w/ P6122 vs P6522...


So if you believe in the overall anisotropy of the universe 
(neglecting the weak interaction), it is time for some more P6(5)22 
examples.


Similarly, you should bring a bomb on your next airplane flight (but 
don't detonate it), because the probability that there will be two on 
any flight is astronomically low.



Hmm - if it was my data - I would probably go with P6522.  While the 
probability is higher for P6122, the maximum likelihood is if the data 
were mine - it would not go with the majority.


With regards to the bomb on a plane... This is an interesting service I 
can offer... By my taking a bomb on a plane - I can pretty much 
guarantee there not be another one there - so all the passengers 
benefit. But what is the probability that I will get the bomb on the 
plane - without getting caught?  If I fail to get it on the plane - have 
I really done anyone a service? (well besides giving the media something 
to report on, the police who get to wave their guns around, etc.).


Ezra

[ccp4bb] Postdoctoral fellowship in Stockholm

[Tien-Chye Tan]

Postdoctoral fellowship in functional studies of membrane-bound enzymes
 
Opening for a postdoctoral research fellow to join the Structural Biology
group at the Division of Glycoscience, KTH Biotechnology (Royal Institute of
Technology), Stockholm, Sweden.
 
We are looking for an highly motivated, enthusiastic person to join a new
research effort on structure-function studies of membrane proteins, in
particular membrane-bound enzymes involved in polysaccharide biosythesis.
 
The suitable candidate is a molecular biologist or biochemist with
documented expertise in gene cloning and recombinant protein expression
using prokaryotic and/or eukaryotic hosts. Expertise in protein purification
and analysis is also required. Experience from work with membrane proteins,
lipid biochemistry, in-vitro translation protein production and/or various
biophysical methods is considered a strong advantage, but not a
prerequisite.
 
The applicant must be able to certify the he/she holds a PhD degree at the
time for the application. Excellent knowledge of spoken and written English
is an absolute requirement.
 
The fellowship is offered for up to two years. General requirements to be
eligible for this position are non-Swedish citizenship and a Doctoral degree
(PhD) from a University outside Sweden.
 
Starting date: available immediately
 
Please send your Curriculum Vitae, list of publications, and the names and
email addresses for 2-3 references to: di...@biotech.kth.se
  before October 15 2009.
 
Inquiries are directed to:
Dr. Tien-Chye Tan
Email: ta...@kth.se
Phone: +46-73-842 56 95
 
Christina Divne, Assoc. Prof.
Glycoscience, KTH Biotechnology, Stockholm, Sweden
Email: di...@biotech.kth.se

URL: www.biotech.kth.se/
URL: www.biotech.kth.se/glycoscience/structure.html

[ccp4bb] AW: [ccp4bb] Ignoring DFIX instructions in the refinement (SHELX)

[Tobias Beck]

Dear Sergii,

>refinement I checked a structure in Coot and all atoms of these 3 molecules
>were separated from each other and on much bigger distances then in DFIX
>instruction

In the header, you have set the connectivity to zero for residues 4001 to
4288. 

CONN 0 O_4001 > O_4288

This is also applied to your small molecules in the channel since in the
.ins file these residues are located in between water 4286 and 4287. The
CONN 0 instruction will activate the antibumping restraints for your LIM
atoms. Therefore they are pushed away from each other.

Either you can change the CONN (and ISOR) instruction and change the order
in the .ins file (move the LIM residues to the end). Or (as I would do it):
insert the LIM residues just after the protein chains, renumber the
waters/LIM and change CONN (and ISOR) accordingly.

>** MERG code changed to 0 for compatibility with HKLF and BASF parameters
>**
>I know, that if I use BASF-instruction I should have MERG 0, but I do not
>have it at all.

For a regular data set, the MERG 4 instruction should be included in the
header. Friedel opposites will be merged (and all f'' are set to zero).

Hope this helps. 

Best wishes, Tobias.


___

Tobias Beck
Dept. Structural Chemistry
Georg-August University Goettingen
Tammannstr. 4
37077 Goettingen, Germany
phone:  +49 551 39-3068
fax:+49 551 39-22582
net:http://shelx.uni-ac.gwdg.de/tbeck/
___


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von
Sergii Buth
Gesendet: Mittwoch, 9. September 2009 21:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Ignoring DFIX instructions in the refinement (SHELX)

Hello All,

I am working on a structure, which is triple helix with a channel inside
where are present some inclusion compounds.
I started to refine the structure of my protein in REFMAC, then I went to
ShelX to refine occupancy of double conformations and finish my structure.
But in ShelX I faced a few problems, and some of them I can not solve by
myself:

1) I have 3 unknown identical inclusion compounds in the channel. I built
the probable structure of the molecule from electron density map (crystal
diffracts up to 1.34 A), then generated for it an idealized PDB file and a
topology file. Then I fit this probable molecule in each of three positions,
found proper atom coordinates for each position, and updated with this
information main PDB file.
Then I refined (isotropically)... And now the problem starts... After
refinement I checked a structure in Coot and all atoms of these 3 molecules
were separated from each other and on much bigger distances then in DFIX
instruction. After Real space refinement in Coot (for this procedure I
imported REFMAC topology to Coot) the atoms stuck together for entire
molecule.
Then ->ShelX refinement-> Coot - and the same - I see separate atoms...

2) And I am wondering about one more warning:

** MERG code changed to 0 for compatibility with HKLF and BASF parameters **
I know, that if I use BASF-instruction I should have MERG 0, but I do not
have it at all.
But I also know, that "the reflections are always merged, and Friedel
opposites combined, before performing Fourier calculations in SHELXL so that
the (difference) electron density is real and correctly scaled."
Does it mean, that I should have MERG instruction anyway?

Please, find attached .ins file for more clarity. (Change extension to .ins,
'coze my proxy blocks it)

Thank you very much for your help,

Best regards, Sergii Buth

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[William G. Scott]

On Sep 8, 2009, at 4:29 PM, Ezra Peisach wrote:

If you want to gamble - go w/ P6122... Data from the PDB  indicates  
that there are 1.5x as many proteins w/ P6122 vs P6522...


So if you believe in the overall anisotropy of the universe  
(neglecting the weak interaction), it is time for some more P6(5)22  
examples.


Similarly, you should bring a bomb on your next airplane flight (but  
don't detonate it), because the probability that there will be two on  
any flight is astronomically low.

[ccp4bb] ctruncate

[Ricardo Aparicio]

Dear all,

For the same input in a ccp4i (v .2.0.4) Scala (v. 3.3.9) job I have 
obtained the following:


with CTRUNCATE (v. 1.0.01)
==
Col SortMinMaxNum  % Mean Mean   Resolution   
Type Column
num order   Missing complete  abs.   Low
High   label


5 BOTH ?   ?  125860.00  ??  -999.00   0.00   F  
F_BA2


with TRUNCATE (v. 6.1)
==
5 NONE1.8   152.8   766   93.9120.2620.26  24.93   2.80   F  
F_BA2



The final file after Ctruncate cannot be read in by some programs 
although  mtzdump can dump it.


Thanks for any comments on possible reasons for this problem.

Ricardo

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[Rafael Couñago]

Thanks for all the replies.

I guess there's no easy way to distinguish between the two space groups 
before obtaining an electron density map.


Cheers.

Rafael.

Eleanor Dodson wrote:

Rafael Couñago wrote:
  

Hi,

I am in doubt between the enamtiomorph space groups, p6522 and p6122. 
Is there a way to distinguish the correct one in the absence of a 
molecular replacement model?


Cheers.

Rafael.




No is the short answer..
If you have heavy atom data with anomalous scattering you will get 
better maps in one than the other..

Eleanor


  

Re: [ccp4bb] Help with improving these crystals

[Janet Newman]

Hi

One of the easiest things to try is in-situ proteolysis - chymotrypsin (1:1000 
or so, we add 1ul of a 1mg/ml solution of chymotrypsin in H20 to about 100ul of 
protein solution) is the classic - mix the protease with the protein and then 
set up as normal.  Of course you can try other proteases as well.  I would 
generally not recommend subtilisin or proteinase K - these are almost 
guarenteed to turn your protein into amino acid soup.

Matrix seeding (Allan D'Arcy is the lead author on the reference for this)  
with the crystals you have is another relatively painless thing to try (ie, use 
your crystals to seed into a screening experiment) - given that your condition 
is ammonium sulfate based, be aware that you will get lots of lovely crystals 
in any screening condition containing calcium.

may the force be with you

Janet



From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Narayanan 
Ramasubbu [ramas...@umdnj.edu]
Sent: 10 September 2009 01:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help with improving these crystals

Dear All:
We have been struggling to improve the crystals shown in the attachment.
These crystals form from a protein solution 8 mg/mL (before drop), drop
sizes are 2 microL of protein + 2 microL of well solution (0.1 MES
buffer, pH 6.5, 1.8 M Ammonium sulfate with 12 mM CoCl2).

The protein was dissolved initially in 20 mM Tris.HCl, pH 8.0 containing
1 mM EDTA.

Low cobalt also gives smaller crystals. These diffract up to 8 A.

Any suggestions to improve these crystals would be most welcome.

Subbu

PS: We have used many additives (Hampton Research - including detergent
additives) to alter the morphology but with little success.

Re: [ccp4bb] Off topic: Purification steps

[Rajendra Singh]

Dear Ronaldo!

I think this should be very straight forward, Generally, after Ni-column
protein can be digested with TEV (1:50, or 1:100 ratio) either at room
temperature or at 4C depending on the stability of the protein. I had tried
this at room temperature, overnight cleavage at 1:100 (TEV: Substrate)
ratio. After TEV digest you can load it onto the His-trap column again by
reducing the concentration of Imidazole by half or 1/3rd of the original
concentration at which protein was eluted. TEV digested protein will remain
unbound to His-trap column and will be in flow through. TEV with his tag
will remain bound to Ni-column. Finally Imidazole can be removed during the
concentration process by buffer exchange.

Raj
On Wed, Sep 9, 2009 at 8:48 AM,  wrote:

> Dear CCP4bb users (this is an off-topic question),
>
> We have a few proteins being expressed as
> HIS-TAG_(TEV_cleavage_site)_PROTEIN
> and we are about to initiate the purification steps.
>
> We have already used the HiTrap-Chelating columns from GE for the first
> purification step (affinity chromatography) and we would like to move
> forward
> with TEV digestion and a second purification step.
>
> We know these following steps are very protein-dependent, but we were
> wondering
> one could share his/her experience in the following steps: removal of
> imidazole,
> cleavage protocol and cleavage identification, second chromatography, etc.
>
> Any experience would be appreciated.
>
> Thanks in advance
>
> Ronaldo.
>



-- 
Rajendra Kumar Singh

Re: [ccp4bb] Help with improving these crystals

[artem]

Beyond improvement via 'chemical' means, I would heartily recommend
mutagenesis for crystal packing improvement. I would be glad to help you
with the latter if you're interested.

Artem

> Dear All:
> We have been struggling to improve the crystals shown in the attachment.
> These crystals form from a protein solution 8 mg/mL (before drop), drop
> sizes are 2 microL of protein + 2 microL of well solution (0.1 MES
> buffer, pH 6.5, 1.8 M Ammonium sulfate with 12 mM CoCl2).
>
> The protein was dissolved initially in 20 mM Tris.HCl, pH 8.0 containing
> 1 mM EDTA.
>
> Low cobalt also gives smaller crystals. These diffract up to 8 A.
>
> Any suggestions to improve these crystals would be most welcome.
>
> Subbu
>
> PS: We have used many additives (Hampton Research - including detergent
> additives) to alter the morphology but with little success.
>

Re: [ccp4bb] Help with improving these crystals

[Jim Fairman]

Have you tried microseeding or macroseeding?  The original crystals
for my Ph D project only diffracted to ~8 angstroms.  Microseeding
gave crystals that eventually diffracted to ~2.0.

Here are two refs that might be useful:

Bergfors, T. (2003). "Seeds to crystals." J Struct Biol 142(1): 66-76.

Luft, J. R. and G. T. DeTitta (1999). "A method to produce microseed
stock for use in the
crystallization of biological macromolecules." Acta Crystallogr D Biol
Crystallogr 55(Pt 5): 988-93.


On Wed, Sep 9, 2009 at 11:36 AM, Narayanan Ramasubbu wrote:
> Dear All:
> We have been struggling to improve the crystals shown in the attachment.
> These crystals form from a protein solution 8 mg/mL (before drop), drop
> sizes are 2 microL of protein + 2 microL of well solution (0.1 MES buffer,
> pH 6.5, 1.8 M Ammonium sulfate with 12 mM CoCl2).
>
> The protein was dissolved initially in 20 mM Tris.HCl, pH 8.0 containing 1
> mM EDTA.
>
> Low cobalt also gives smaller crystals. These diffract up to 8 A.
>
> Any suggestions to improve these crystals would be most welcome.
>
> Subbu
>
> PS: We have used many additives (Hampton Research - including detergent
> additives) to alter the morphology but with little success.
>



-- 
Jim Fairman
Postdoctoral Research Assistant
Case Western Reserve University
216-368-3337 jxf...@case.edu

[ccp4bb] Team Leader Position at EMBL, Hamburg Unit

[Margret Fischer]

Dear All,
there is a job vacancy at the EMBL Hamburg for the following position:

*Team Leader Computational Infrastructures and Applications*

EMBL is building an integrated facility in structural biology at the
new PETRA-3 synchrotron ring at DESY, Hamburg, Germany. The optical
properties of PETRA-III will allow the operation of world-class
synchrotron radiation beamlines from 2010/11, providing an ideal
research environment for future challenges in structural biology.

We are looking for a Team Leader who will manage the local computer
group at EMBL-Hamburg and develop novel software and associated
infrastructure in cooperation with the researchers (e.g. for access to
remote experiments, particularly for the synchrotron beamlines at
PETRA-3 and the crystallisation facility). (S)he will administer and
further develop the local network, database administration and web
services using state-of-the-art technologies with a focus on a
user-friendly scientific computer environment. The post holder also
supervises and participates in installation, maintenance and development
of applications for the outstation's scientific user support, advanced
training and research projects. Candidates should hold a PhD in a
relevant field, have strong records in computational research and high
level scientific/technical accomplishments.

For a complete job description and to apply please visit: www.embl.org/jobs

[ccp4bb] Purified Membrane Protein Samples for CrystalJet

[Patrick W. Cooley]

We are developing a prototype inkjet based crystal screening platform (NIH
SBIR funded). 

Details regarding the system are posted here:

http://www.microfab.com/equipment/pdf/CrystalJet_Handout_rev3.pdf

I'm looking for purified membrane protein samples to further validate the
system. Please let me know if you have samples available.

Thank you.

Patrick

Re: [ccp4bb] Off topic: Purification steps

[Ralf JAUCH]

Hi Ronaldo,

We immediately desalt after His-Trap (desalting column connected in series) 
into an Imidazol free and low salt buffer and digest with 1:50 to 1:100 
TEV:substrate ratios (w:w) at RT or in the cold room (time often a compromise 
between protein precipitation and completion of the cut) before proceeding to 
ion exchange and size exclusion chromatography.


cheers,

Ralf




-Original Message-
From: CCP4 bulletin board on behalf of na...@icb.ufmg.br
Sent: Wed 9/9/2009 8:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off topic: Purification steps
 
Dear CCP4bb users (this is an off-topic question),

We have a few proteins being expressed as HIS-TAG_(TEV_cleavage_site)_PROTEIN
and we are about to initiate the purification steps.

We have already used the HiTrap-Chelating columns from GE for the first
purification step (affinity chromatography) and we would like to move forward
with TEV digestion and a second purification step.

We know these following steps are very protein-dependent, but we were wondering
one could share his/her experience in the following steps: removal of imidazole,
cleavage protocol and cleavage identification, second chromatography, etc.

Any experience would be appreciated.

Thanks in advance

Ronaldo.

[ccp4bb] Off topic: Purification steps

[nagem]

Dear CCP4bb users (this is an off-topic question),

We have a few proteins being expressed as HIS-TAG_(TEV_cleavage_site)_PROTEIN
and we are about to initiate the purification steps.

We have already used the HiTrap-Chelating columns from GE for the first
purification step (affinity chromatography) and we would like to move forward
with TEV digestion and a second purification step.

We know these following steps are very protein-dependent, but we were wondering
one could share his/her experience in the following steps: removal of imidazole,
cleavage protocol and cleavage identification, second chromatography, etc.

Any experience would be appreciated.

Thanks in advance

Ronaldo.

[ccp4bb] Postdoc position in drug discovery - King's College London

[Beavil, Andrew]

A 2+ year industry funded post-doctoral research assistant position suitable
for an experienced protein crystallographer is available at King's College
London.

The project in the laboratory of Andrew Beavil and Brian Sutton involves
structure based drug discovery for the inhibition of an important
protein-protein interaction.

 

For details, please see the advertisement on:

http://www.kcl.ac.uk/depsta/pertra/vacancy/external/pers_detail.php?jobindex
=8162

[NB full job description in the web link at the bottom of the page]

 

Closing date 17th September.

 

 

 

 

--

-

Dr. Andrew J. Beavil,Phone: (+44) (0)20 78488064

(Asthma UK funded Senior Lecturer in Asthma) Fax  : (+44) (0)20 78486410

 

MRC & Asthma UK Centre in Allergic Mechanisms of Asthma 

King's College London, 

The Randall Centre,

New Hunt's House, Email: andrew.bea...@kcl.ac.uk

Guy's Campus,

London Bridge,

London. SE1 1UL

-

 



smime.p7s
Description: S/MIME cryptographic signature

[ccp4bb] Postdoc position at GlaxoSmithKline

One year postdoctoral scientist position at GlaxoSmithKline (Stevenage - 
just north of London)

An exciting opportunity exists to join a successful team working 
on the structure and function of a new class of antibacterials within 
GlaxoSmithKline. Structural studies are being used to guide chemistry. 
High resolution crystal structures have shown the binding mode for the 
compounds, but growing well diffracting crystals of target proteins 
continues to be challenging. The primary role of the post-doc will be to 
drive forward the structural and functional studies on target proteins by 
focusing on developing robust crystallisation systems. The person 
appointed will work closely with members of protein biochemistry and 
computational and structural chemistry groups, and will be involved in 
characterising complexes (using various biochemical and biophysical 
techniques) and crystallising and solving crystal structures.
Candidates should have experience in at least three of the 
following: protein  purification, characterisation, biophysics (including 
nmr), crystallisation or crystallography. Candidates should have good 
communication skills and enjoy working in a multi-disciplinary 
environment. 

Application on line at:

https://careers.peopleclick.com/careerscp/client_gsk/external_pages_uk/gateway.do?functionName=viewFromLink&jobPostId=148927&localeCode=en-us

Dr. Benjamin Bax
GlaxoSmithKline 
Medicines Research Centre
Gunnels Wood Road
Stevenage
Hertfordshire, SG1 2NY
UK

E-mail: benjamin.d@gsk.com
---
This e-mail was sent by GlaxoSmithKline Services Unlimited 
(registered in England and Wales No. 1047315), which is a 
member of the GlaxoSmithKline group of companies. The 
registered address of GlaxoSmithKline Services Unlimited 
is 980 Great West Road, Brentford, Middlesex TW8 9GS.
---

Re: [ccp4bb] Distinguishing between P6(5)22 and P6(1)22

[Eleanor Dodson]

Rafael Couñago wrote:

Hi,

I am in doubt between the enamtiomorph space groups, p6522 and p6122. 
Is there a way to distinguish the correct one in the absence of a 
molecular replacement model?


Cheers.

Rafael.



No is the short answer..
If you have heavy atom data with anomalous scattering you will get 
better maps in one than the other..

Eleanor

Re: [ccp4bb] purchasing heavy atom clusters

[Claus Flensburg]

Hi Engin,

On Tue, Sep 08, 2009 at 04:06:20PM -0700, Engin Ozkan wrote:
...
> On a related point, I would appreciate any pointers, especially on  
> software like shelx, sharp, solve, and mlphare, on treating clusters at  
> resolutions where the heavy atoms are not resolved (at 6A or worse).  
> Until now, I've had much better luck just working on the Patterson  
> myself, and heavy atom searches and heavy atom position refinement with  
> software seem to invariably mess up the sites. Treating heavy metal  
> clusters as point scatterers is the preferred way in the literature, but  
> this could be implemented a few different ways. Any opinions are  
> appreciated.

SHARP has a feature whereby a cluster can be treated like a point
scatterer with a scattering factor that is the spherical average
of the atoms. The usage is briefly described here:

http://www.globalphasing.com/sharp/manual/appendix3.html#generalSPHCLUSTER


Regards,

ClAuS

[ccp4bb] Postdoc Positions in Structural Biology at Astex Therapeutics

[Marc O'Reilly]

Career Opportunities at Astex - September 2009 

Astex Therapeutics Ltd, based in Cambridge, UK, was founded 10 years ago
and is a world-leading biotechnology company that has pioneered
fragment-based drug discovery (FBDD) platform to discover and develop
medicines in areas of unmet medical need. Astex has successfully
progressed its first three oncology drug candidates into clinical trials
and has recently extended its technology to anti-viral targets.
Astex has established an internationally leading scientific reputation
in FBDD, the most important new area of drug discovery chemistry in the
last 20 years. We remain committed to the highest possible scientific
standards and have established a strong track record in high calibre
scientific publications, presentations and peer citations.
As a result of this continued success in our drug discovery programmes,
we are now seeking highly talented scientists with a passion for
innovative drug discovery.
The closing date for applications is 25th September 2009.

Postdoctoral Structural Biologists (SB-09) 

These roles are 2 year Post-Doc positions for lab-based scientists to
join our structural biology department, which represent a tremendous
learning experience at the start of a career in drug discovery,
including interaction with scientists in other disciplines in the
company's well equipped structural biology laboratories.
Candidates will have broad skills in molecular biology, protein science
and protein structure determination. Familiarity with insect cell
expression systems and with protein purification - characterisation is
desirable. Ideally you will have recently completed a PhD or have
several years of relevant postgraduate experience.

Salaries and benefits package are highly competitive to ensure we
attract, motivate and retain the best candidates.  Please send your
application to: 
Human Resources
Astex Therapeutics Ltd
436 Cambridge Science Park
Milton Road
Cambridge
CB4 0QA
UK
Or apply by e-mail to: h...@astex-therapeutics.com



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Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
Cambridge CB4 0QA under number 3751674