[ccp4bb] CCP4 Study Weekend: From Crystal to Structure with CCP4

[Charles Ballard]

We cordially invite you to participate in this year's Study Weekend  
at the East Midlands Conference Centre, University of Nottingham. The  
annual CCP4 Study Weekend is a chance to shake off the post-New Year  
torpor, and work hard and play hard with your fellow  
crystallographers. Once again, we have put together an exciting  
scientific programme for Thursday and Friday, either side of the  
traditional conference dinner. Please also check out the satellite  
meetings which may be of interest. The Study Weekend is a chance to  
catch up with old friends, but is also a chance to meet the CCP4  
staff who will be there in force to demonstrate the latest software  
and to answer questions - please say hello!


This year, the topic for the Study Weekend is "From Crystal to  
Structure with CCP4". In keeping with previous CCP4 meetings, the  
lectures will focus on the presentation and discussion of advanced  
methods and techniques developed and used by the leaders in the field.


Registration and conference information can be found at

http://www.cse.scitech.ac.uk/events/CCP4_2010/

Scientific Organisers
Keith Wilson - University of York (UK)
Kevin Cowtan - University of York (UK)
Paul Emsley - University of Oxford (UK)

Administrative Organisers from STFC, Daresbury Laboratory
Shirley Miller (shirley.mil...@stfc.ac.uk)
Damian Jones (damian.jo...@stfc.ac.uk)
Laura Johnston (laura.johns...@stfc.ac.uk)

Financial Enquiries
Tracey Kelly - (tracey.ke...@stfc.ac.uk)

Registration Fee
We will operate a two-tiered registration fee, which benefits those  
who register early! The registration fee includes all meals during  
the conference, including the conference dinner on Thursday evening  
at the East Midlands Conference Centre.


Register between 14 September  21 November - the fee is £210
Register between 22 November and 11 December - the fee is £260

REGISTRATION CLOSES ON 12 DECEMBER!

For those applying for a standard bursary (registration fee and one  
night's standard accommodation) the registration fee of £210 is the  
only fee that will apply. Please note that there has been a change to  
the way in which bursaries are awarded from previous years. If you  
are intending to apply for a standard bursary please ensure that you  
read this section.



 

[ccp4bb] Low Bfactor values for waters after TLS

[Alasdair K. Mackenzie]

Greetings CCP4-ers,

I have been running some TLS refinement which does wonders for my R/Rfree
values, but seems to give some spurious Bfactors/ADPs for the waters, e.g.
B= 2.

These low Bfactors appear relatively consistent with the residual protein
B-factors (i.e. the pdb output from REFMAC), but when i use TLS analyse to
apply the TLS contribution to the total B-factors for the model, the low
water B values seem crazy...i apparently have a water with a B-factor
of 2 interacting with a side chain with a B-factor of 60

Has anyone encountered this type of thing before? and does anyone have a
good solution for getting around the problem?

cheers,
Al

Re: [ccp4bb] Low Bfactor values for waters after TLS

[Roberto Steiner]

Hi Alasdair
On 11 Sep 2009, at 09:46, Alasdair K. Mackenzie wrote:


Greetings CCP4-ers,

I have been running some TLS refinement which does wonders for my R/ 
Rfree
values, but seems to give some spurious Bfactors/ADPs for the  
waters, e.g.

B= 2.

These low Bfactors appear relatively consistent with the residual  
protein
B-factors (i.e. the pdb output from REFMAC), but when i use TLS  
analyse to
apply the TLS contribution to the total B-factors for the model, the  
low
water B values seem crazy...i apparently have a water with a B- 
factor

of 2 interacting with a side chain with a B-factor of 60

Has anyone encountered this type of thing before?


Yes.
I have reported this to Garib some time ago and I believe the active  
Refmac people are working on this.




and does anyone have a
good solution for getting around the problem?


Mhh...
Latest Refmac versions seem to consider waters directly bound to the  
protein as members of the various TLS groups.

You can override this by using
TLSD WATERS EXCLUDE

You can give it a go and see if it helps.

Best
Roberto




cheers,
Al

Re: [ccp4bb] Off topic: Purification steps

[ucbccka]

Limitless suggestions, but as you are about to embark on TEV digestion,
one thing you can do is do this within a dialysis tube and 1:20 and
dialyse for the magic period (overnight) to get rid of the imidazole, then
follow this with an IMAC step to remove uncleaved protein and the TEV. 
Remember to equilibrate your IMAC column including a little imidazole
5-30mM because, despite your wanting your tagged stuff to stick, some
proteins stick to the resin anyway if you don't equilibrate.  To make
doubly sure of this I always elute off the beads and run it on a gel, just
to see what is going on.

cheers
charlie

> 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.
>


-- 
Dr Charles Allerston
Associate Research Scientist
Structural Biology
Ark Therapeutics
Darwin Building, UCL
Gower Street,
London WC1H 9EH
United Kingdom

mailto: c.allers...@ucl.ac.uk
phone:  +44 (0)2076791354
Web:www.arktherapeutics.com

Re: [ccp4bb] stabilizing solution

[ucbccka]

Hi,

in this paper

http://journals.iucr.org/d/issues/1999/05/00/gr0904/gr0904.pdf

they seemed to use the protein solution as a stabilising solution.  Seems
like a good idea as you are not diluting your concentrations too much in
that case.

cheers
charlie


> Dear CCP4bbers,
>
> Please comment on the stabilizing solution for seed stocks. If the crystal
> is in 30% MPD and coming after 2-3 days, what should be the stabilizing
> solution for seeding.
> Thanks.
> James
>


-- 
Dr Charles Allerston
Associate Research Scientist
Structural Biology
Ark Therapeutics
Darwin Building, UCL
Gower Street,
London WC1H 9EH
United Kingdom

mailto: c.allers...@ucl.ac.uk
phone:  +44 (0)2076791354
Web:www.arktherapeutics.com

[ccp4bb] September 15th - registration deadline for PSI users meeting j...@p 09 (SLS)

[Rouven Bingel-Erlenmeyer]

Dear SLS users,

I would like to draw your attention to the Joint User Meeting at PSI
(j...@p '09).

Please remember the approaching deadline (*** September 15 ***) for
registration and submission of poster abstracts for the first Joint
Users' Meeting (j...@p '09) of the PSI user facilities SLS, SINQ and SmuS.

The meeting will be organized on October 12-13, 2009 at the Paul
Scherrer Institut, Villigen, Switzerland.

Detailed information about the scientific program and online
registration is available from the meeting website:
http://user.web.psi.ch/jump09/html/index.shtml

Looking forward to meeting you at PSI
Rouven



Further information:

j...@p '09 is a users for users meeting. In fact, both topics and
speakers have been selected by the three user communities.

The aim of this Joint Users' Meeting is to bring together the three user
communities and to generate synergies among the users driven by science
rather than methods.

The meeting will consist of a plenary session, poster sessions and
parallel scientific symposia on the following topics:

 - Colloids and soft condensed matter
 - Correlated electron systems
 - Materials for environment and energy
 - Imaging of biological and technical materials
 - Advanced techniques at PSI large facilities
 - From gene to structure: impact of automation technologies

In addition a PSI medal prize will be awarded for the best recent PhD
thesis work based on experiments done at the PSI user facilities.


--
**
Paul Scherrer Institute
Dr. Rouven Bingel-Erlenmeyer
Swiss Light Source
WSLA 222
5232 Villigen
SWITZERLAND

rouven.bingel-erlenme...@psi.ch
http://sls.web.psi.ch

+41 56 310 5823 phone
+41 56 310 5292 fax
**

[ccp4bb] Alternative conformation in Mac Refmac5

[Heidi Tuominen]

Hi all,

I have updated lately to ccp4-6.1.2. I have Macintosh. Now I have problem with 
alternative conformations. After Refmac5 run all alternative conformation atoms 
are fully unordered without any chemical restraints. If I put same pdb to 
Windows Refmac5.5.0102 there is no any problems except R-factors are some 
higher.

Do I have some problem or is there bug in Mac version of Refmac5.5.0102? How 
problem could be solved?

Thank you,
Heidi Tuominen
University of Turku, Finland

Re: [ccp4bb] Alternative conformation in Mac Refmac5

[Roberto Steiner]

Hi Heidi,

I have noticed the same thing. Went back to Refmac v93 (mac version)  
and side-chains stopped flying. Needs a fix.


Best
Roberto
On 11 Sep 2009, at 10:59, Heidi Tuominen wrote:


Hi all,

I have updated lately to ccp4-6.1.2. I have Macintosh. Now I have  
problem with alternative conformations. After Refmac5 run all  
alternative conformation atoms are fully unordered without any  
chemical restraints. If I put same pdb to Windows Refmac5.5.0102  
there is no any problems except R-factors are some higher.


Do I have some problem or is there bug in Mac version of  
Refmac5.5.0102? How problem could be solved?


Thank you,
Heidi Tuominen
University of Turku, Finland

[ccp4bb] Peg3350 model

[sajid akthar]

Hi All

I have some density and I can fit a peg molecule in their. I am confused and 
when I search database for peg3350, I have no hit. How can I build a model for 
Peg 3350. I found some PDB's with peg; but they they have used peg400; Is there 
any difference in the model between peg3350 and peg400.

Can any one define where the peg ion could bind.

Thanks

Sajid



  Add whatever you love to the Yahoo! India homepage. Try now! 
http://in.yahoo.com/trynew

[ccp4bb] Pernament Beamline Scientist position at Synchrotron SOLEIL

[SHEPARD William]

Dear Fellow Crystallographers, 

 

There is a permanent scientific position opening on the PROXIMA 2
beamline at Synchrotron SOLEIL (see below).  We are looking for
candidates with a background & post-doctoral experience in
macromolecular crystallography and instrumentation. 

 

Please note the the deadline is 30 September 2009.

 

Kind regards, 

William SHEPARD

 



Dr. William SHEPARD

Principal Beamline Scientist PROXIMA II

Synchrotron SOLEIL

L'Orme des Merisiers

Saint Aubin, BP 48 

F-91192 GIF-SUR-YVETTE

France 

tel: +33 1 69 35 96 36

fax: +33 1 69 35 94 56

william.shep...@synchrotron-soleil.fr
 

 

 

 

Beamline Scientist PROXIMA 2 (m/f)

(Ref: EXP-102)

SOLEIL is a state-of-the-art, third generation synchrotron radiation
centre dedicated to scientific research at an international level. The
PROXIMA 2 beamline will feature two undulators in canted geometry
providing for two independent experimental stations dedicated to
biological macromolecular crystallography (MX). The first branch,
PROXIMA 2A, will specialize in the collection of diffraction data from
micro-crystals and will start commissioning in 2010. The second branch,
PROXIMA 2B, is reserved for the future, and its objectives and design
are currently under study. 

 

We are seeking a motivated scientist with a strong background in MX.
Candidates must have hands-on experience working with instrumentation on
synchrotron MX beamlines. The duties will include the installation &
commissioning of the beamline, as well as the development of
methodologies related to micro-crystallography. Computing & programming
skills are desired. Experience in sample preparation and laboratory
techniques will be appreciated. This is a permanent scientific position
in the PROXIMA 2A team with ample opportunities to conduct in-house
research. A Ph.D. degree (or equivalent), plus post-doctoral experience,
in MX and instrumentation is a prerequisite for this position.

 

You will be part of a team of scientists who ensure the construction,
commissioning and smooth functioning of the PROXIMA beamlines. You will
also be expected to conduct research at a high level in a field
pertaining to structural biology employing synchrotron radiation. The
research may be pursued either independently or in collaboration.

 

Applications including the addresses of three referees should be
registered directly on the SOLEIL internet site 
http://candidature.synchrotron-soleil.fr/YourApplication
 .

 

More information is available at

http://www.synchrotron-soleil.fr/portal/page/portal/Soleil/OffresEmplois
/EXP-102

 

Or contact

 

William SHEPARD

tel. +33-1-6935-9636

william.shep...@synchrotron-soleil.fr
 

 

Jean-Pierre SAMAMA

tel. +33-1-6935-9775

jean-pierre.sam...@synchrotron-soleil.fr
 

 

Expiry date for applications: 30 September 2009

 

 

 

 

 

 

 



Dr. William SHEPARD

Principal Beamline Scientist PROXIMA II

Synchrotron SOLEIL

L'Orme des Merisiers

Saint Aubin, BP 48 

F-91192 GIF-SUR-YVETTE

France 

tel: +33 1 69 35 96 36

fax: +33 1 69 35 94 56

william.shep...@synchrotron-soleil.fr
 

 

 

 

<>

[ccp4bb] Molecular replacement with merohedarlly twinned data

[Pietro Roversi]

Dear all,
when searching in Molecular Replacement
against say perfectly merohedrally twinned data (i.e. an alpha=0.5 twin)
do I understand it right that I should expect two sets of solutions
that are equivalent under the twin operator (bar xtal symmetry and/or
origin shifts)?

Thanks!

Ciao

Pietro
-- 
Pietro Roversi
EP Abraham Fellow in Biochemistry - Lincoln College - Oxford
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3RE, England UK
Tel. 0044-1865-275385

[ccp4bb] configure.def not copied over with in-place update of ccp4

[hari jayaram]

Hi I just updated my ccp4 to 6.1.2 ( the August 13th 2009  release) and
thought I would pass on this feedback.

I used the source version and the built in install.sh script which worked
very well on ubuntu Linux 654 bit ( Hardy Heron)

However after the update the new ccp4i gui had lost the location of all my
projects , although it still remembered the names.

The installation script did not move my old configure.def into the  new
installation. So I had to manually copy the old configure.def over and
change the
value as mentioned in a previous post on ccp4bb

USE_DBCCP4I_ON_STARTUP_logical  0


Hope this helps someone
else
Hari

[ccp4bb] BM14 beamtime for the period November - December 2009

[hassan belrhali]

   Dear all,

the period of November - December 2009 is opened for proposal submissions

for beamtime at the BM14 MAD MX Beamline (ESRF, Grenoble, France) .

Thank you to submit your proposal on-line http://www.bm14.eu  (“Apply for
Beamtime”).

We provide funding for EU-member and EU-associated state users for travel
and subsistence.

*Beamline features:*

-  Easily tuneable energy over 7 to 17 keV

-  MarMosaic 225 CCD detector

-  MD2 Microdiffractometer with mini-Kappa goniometer head

-  Robotic Sample changer (SPINE standard sample holders are
mandatory)

*NEW:*

-  Very low resolution beamstop: permits diffraction to be recorded
down to 300 Å

-  Crystal Humidity Control Device (HC1) as a tool for improving
diffraction quality

   (Upon request:
http://www.embl-grenoble.fr/groups/instr/humidifier_page1.html).

-  Remote data collection.

Best regards,

Hassan Belrhali (belrhali-at-embl.fr ).

Re: [ccp4bb] Low Bfactor values for waters after TLS

[Huw Jenkins]

On 11 Sep 2009, at 09:46, Alasdair K. Mackenzie wrote:


I have been running some TLS refinement which does wonders for my R/ 
Rfree
values, but seems to give some spurious Bfactors/ADPs for the  
waters, e.g.

B= 2.


I am getting this too but not just for waters - some example lines  
from the pdb files output when the same input files are refined with  
REFMAC 5.2.0019 (CCP4 6.0) and Refmac_5.5.0102 (CCP4 6.1)


In all cases 10 cycles TLS refinement followed by 10 cycles  
restrained refinement.  TLS groups (5) as suggested by TLSMD were  
defined by a TLSIN file and the TLS parameters were initialised to zero.



REMARK   3   PROGRAM : REFMAC 5.2.0019
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  :5
REMARK   3   ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM  1  N   GLY A   1  57.296 -46.837  36.250  1.00  
30.89   N
ATOM  2  CA  GLY A   1  57.071 -47.826  37.339  1.00  
29.53   C
ATOM  3  C   GLY A   1  55.665 -48.421  37.355  1.00  
28.37   C
ATOM  4  O   GLY A   1  55.248 -49.012  38.369  1.00  
30.06   O
ATOM  5  N   ARG A   2  54.946 -48.312  36.249  1.00  
26.00   N
ATOM  6  CA  ARG A   2  53.537 -48.738  36.223  1.00  
24.66   C
ATOM  7  CB  ARG A   2  52.894 -48.328  34.894  1.00  
25.61   C
ATOM  8  CG  ARG A   2  52.791 -46.825  34.732  1.00  
30.86   C
ATOM  9  CD  ARG A   2  51.932 -46.448  33.555  1.00  
35.59   C
ATOM 10  NE  ARG A   2  52.688 -46.482  32.319  1.00  
40.25   N
ATOM 11  CZ  ARG A   2  53.137 -45.407  31.681  1.00  
42.01   C
ATOM 12  NH1 ARG A   2  52.900 -44.188  32.148  1.00  
41.24   N
ATOM 13  NH2 ARG A   2  53.829 -45.563  30.561  1.00  
44.36   N
ATOM 14  C   ARG A   2  53.418 -50.252  36.366  1.00  
23.17   C
ATOM 15  O   ARG A   2  54.313 -51.001  35.902  1.00  
22.56   O
ATOM 16  N   SER A   3  52.314 -50.708  36.961  1.00  
20.25   N
ATOM 17  CA  SER A   3  52.008 -52.147  36.927  1.00  
19.82   C
ATOM 18  CB  SER A   3  50.706 -52.452  37.673  1.00  
20.71   C
ATOM 19  OG  SER A   3  49.601 -51.837  37.041  1.00  
20.34   O
ATOM 20  C   SER A   3  51.851 -52.647  35.501  1.00  
19.77   C


REMARK   3   PROGRAM : REFMAC 5.5.0102
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  :5
REMARK   3   ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM  1  N   GLY A   1  57.316 -46.814  36.305  1.00  
12.20   N
ATOM  2  CA  GLY A   1  57.070 -47.790  37.390  1.00   
8.55   C
ATOM  3  C   GLY A   1  55.665 -48.410  37.347  1.00   
6.78   C
ATOM  4  O   GLY A   1  55.239 -49.035  38.362  1.00  
10.43   O
ATOM  5  N   ARG A   2  54.969 -48.342  36.238  1.00   
3.00   N
ATOM  6  CA  ARG A   2  53.526 -48.722  36.241  1.00   
2.00   C
ATOM  7  CB  ARG A   2  52.865 -48.356  34.895  1.00   
2.17   C
ATOM  8  CG  ARG A   2  52.837 -46.851  34.750  1.00   
8.65   C
ATOM  9  CD  ARG A   2  51.980 -46.398  33.603  1.00  
12.50   C
ATOM 10  NE  ARG A   2  52.692 -46.488  32.373  1.00  
20.40   N
ATOM 11  CZ  ARG A   2  53.158 -45.450  31.693  1.00  
22.50   C
ATOM 12  NH1 ARG A   2  52.983 -44.201  32.118  1.00  
18.27   N
ATOM 13  NH2 ARG A   2  53.819 -45.694  30.575  1.00  
23.75   N
ATOM 14  C   ARG A   2  53.413 -50.249  36.396  1.00   
2.00   C
ATOM 15  O   ARG A   2  54.309 -51.009  35.916  1.00   
2.00   O
ATOM 16  N   SER A   3  52.311 -50.700  36.987  1.00   
2.00   N
ATOM 17  CA  SER A   3  52.014 -52.145  36.912  1.00   
2.00   C
ATOM 18  CB  SER A   3  50.694 -52.464  37.655  1.00   
2.00   C
ATOM 19  OG  SER A   3  49.581 -51.843  37.061  1.00   
2.00   O
ATOM 20  C   SER A   3  51.876 -52.639  35.489  1.00   
2.00   C



If I include the keywords "TLSD WATERS EXCLUDE" it doesn't fix the  
problem:


REMARK   3   PROGRAM : REFMAC 5.5.0102
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  :5
REMARK   3   ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
ATOM  1  N   GLY A   1  57.282 -46.747  36.351  1.00   
8.67   N
ATOM  2  CA  GLY A   1  57.095 -47.808  37.373  1.00   
5.77   C
ATOM  3  C   GLY A   1  55.679 -48.420  37.348  1.00   
4.19   C
ATOM  4  O   GLY A   1  55.251 -49.030  38.375  1.00   
7.25   O
ATOM  5  N   ARG A   2  54.970 -48.346  36.248  1.00   
2.00   N
ATOM  6  CA  ARG A   2  53.529 -48.731  36.249  1.00   
2.00   C
ATOM  7  CB  ARG A   2  52.864 -48.370  34.899  1.00 

Re: [ccp4bb] Molecular replacement with merohedarlly twinned data

[Randy Read]

Yes, but if the twin fraction deviates even slightly from 1/2, you may  
only get one solution from the search.  If you want, you can generate  
the other one and see how happy the program is.


Regards,

Randy

On 11 Sep 2009, at 15:12, Pietro Roversi wrote:


Dear all,
when searching in Molecular Replacement
against say perfectly merohedrally twinned data (i.e. an alpha=0.5  
twin)

do I understand it right that I should expect two sets of solutions
that are equivalent under the twin operator (bar xtal symmetry and/or
origin shifts)?

Thanks!

Ciao

Pietro
--
Pietro Roversi
EP Abraham Fellow in Biochemistry - Lincoln College - Oxford
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3RE, England UK
Tel. 0044-1865-275385


--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www- 
structmed.cimr.cam.ac.uk

[ccp4bb] Announcement: Beta test of software for picking compounds for binding analysis

[John Badger]

The SDsearch application is intended to allow crystallographers and other 
structure analysts quickly find analogs of known ligands or build small 
fragment/scaffold libraries without incurring the cost or requiring the 
technical 
resources needed to establish commercial database software. For example, 
the software could be used to find sets of compounds related to ligands found 
in earlier crystal structure analysis that might be candidates for testing for 
binding in ongoing experiments.

The software is geared to efficiently search and cherry-pick from the large 
collections of compounds available from commercial chemical vendors. Search 
criteria include chemical properties (molecular weight, numbers of H-bond 
donors, acceptors, polar surface area, solubility, numbers of rotatable bonds) 
and chemical substructures (for example, particular cores or side groups). The 
software has been successfully used to create small libraries of low molecular 
weight compounds ('fragments' or 'scaffolds') for screening by crystallography 
and activity assay.

The current version of this software runs on Windows but other OS support 
may follow. The software is available for testing by either academic or 
commercial researchers. 

Please contact info1.dgt...@gmail.com (not my email!) in order to obtain the 
distribution.