[ccp4bb] Engineering Associate Position in Robotics + Miniaturization, Trinity College Dublin

[Martin Caffrey]

Engineering Associate  -  Robotics, Sensors and Miniaturization

Membrane Structural and Functional Biology Group

School of Biochemistry and Immunology

Trinity College Dublin, Ireland

An exciting opportunity exists for a top Engineer to join this 
multidisciplinary team to characterize and improve the performance of existing 
crystallization and imaging robots, and to extend their applicability into new 
research areas such as microarrays and sensors.  The project will involve 
development of novel sensors and crystal imaging, harvesting and manipulation 
robots.  Miniaturization is a constant goal given that the biomaterials used 
are expensive and in short supply.

For the highly motivated individual, it is possible to pursue part-time an 
advanced degree on a research topic relevant to the position advertised.

Required

* A B.Sc. or M.Sc. or equivalent qualification in a relevant 
engineering and/or physical/life science  

* 1 - 2 years experience in instrument development/testing and computer 
interfacing

* High self-motivation and detail oriented with a keen interest in 
applying engineering principles to the basic sciences   

* Experience in troubleshooting and interfacing components and computers

* Desire to learn and to work on a variety of bio-techniques

* Demonstrated ability to achieve results on time and on target

* Good analytical ability, and reasoning and organization skills

* Good written and verbal communication skills

* Evidence of working as part of a team and commitment to team work

Desired

* Experience in automation, integration and LIMS

* Experience writing software drivers in .NET or C# platforms for 
integrating third party components into the system

* Knowledge of SQL, database packages, and LabView 

* Knowledge of image processing tools for use in robot performance 
evaluation

* Experience of basic machining and electronics, and AutoCAD

* Knowledge of basic chemistry and/or biochemistry laboratory procedures

Closing Date:  Until position is filled.  

Contract Type: Specified Purpose  

Salary Range: € 24,952 - € 40,449 per annum

Principal Investigator: Prof. Martin Caffrey - martin.caff...@tcd.ie 

Further information and application material available from: 
http://www.tcd.ie/vacancies/external/JS_ResearchAssistant_BiochemistryImmunology_Jan10.php

--

Martin Caffrey

School of Biochemistry and Immunology

Trinity College Dublin

Unit 16, Trinity Technology and Enterprise Centre

Pearse Street

Dublin 2, Ireland

Email:   martin.caff...@tcd.ie

Cell Phone: + 353  (0) 86  818  7704

Office Phone: + 353  (0) 1  896  4253

 

[ccp4bb] Persistent Twinning

[George DeTitta]

Can anybody point me to a protein, or proteins, that can be crystallized but
only as a twinned crystal, even after repeated tries?  At this point the
type of twinning is unimportant, but I'm particularly interested in
non-merohedrally twinned protein crystals.  Many thanks.  GDT

[ccp4bb] two multmeric species in solution

[Claudine MAYER]

Hi all,

We have recently solved a structure that is a crystallographic dimer. We
have performed UCA experiments and we observe a monomer/dimer distribution
in nearly equal proportion. This distribution does not change with protein
concentration, meaning that the two species are not in equilibrium. There
is no structural differences between the dimer and the monomer.

We would be interested in similar cases, eg coexistence of 2 multimers
without exchange between the 2 forms. Does somebody have any explanation ?

Thank you

cheers
claudine



Pr Claudine MAYER


Université Paris Diderot - Paris 7

Dynamique structurale des Macromolécules
Département de Biologie Structurale et Chimie
Institut Pasteur
25 rue du Dr Roux
75 015 PARIS
Tel. 01 45 68 83 87
Mobil. 06 07 23 51 16
Fax. 01 45 68 89 93
Mail. ma...@pasteur.fr

Re: [ccp4bb] problem with Coot:findwaters in ccp4i

[Tim Gruene]

Hi Paula,

did you check if Coot/bin is in the PATH variable when you start ccp4i? 
Maybe the coot executable you run is a wrapper that sets the path which is 
not done as you start ccp4i.


Try to type 'findwaters' from the same terminal you start ccp4i from. Does 
that yield a 'command not found'?


Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Tue, 19 Jan 2010, Paula Salgado wrote:


Hi everyone

I just downloaded and installed the newest ccp4i release, including Coot
0.6.0. It all seemed fine, except when I try to run refmac from ccp4i,
using the "Run Coot:findwaters", process fails with error message;

**

The program run with command: findwaters --pdbin
"/tmp/psalgado/test_pdb_1.tmp" --hklin "/tmp/psalgado/test_mtz_1.tmp" --f
DELFWT --phi PHDELWT --pdbout "/tmp/psalgado/test_1.tmp" --sigma 2.0

has failed with error message

couldn't execute "findwaters": no such file or directory

***


#CCP4I TERMINATION STATUS 0 "couldn't execute "findwaters": no such file
or directory"

#CCP4I TERMINATION TIME 19 Jan 2010 12:39:26

#CCP4I MESSAGE Task failed



I checked and the Coot/bin directory exists and it contains a
"findwaters" executable file.

I should add that doing "find waters" within Coot works fine.


Any ideas? All help welcomed.


Thanks!

Paula

=

 Dr Paula Salgado

 Division of Molecular Biosciences
 Department of Life Sciences
 Faculty of Natural Sciences
 Biochemistry Building, 5th Floor
 Imperial College London
 South Kensington Campus
 SW7 2AZ
 London

Tel: 02075945464
Fax: +44 (0)20 7594 3057

Re: [ccp4bb] two multmeric species in solution

[Anastassis Perrakis]

Hi -

Could the dimer in solution be mediated by an intra-molecular Cys  
bridge?


A.

PS I would think that you are maybe a bit too deterministic in your  
conclusion ... would it not be better to say that 'the equilibrium  
between monomer-dimer does not change in the range of conditions we  
tried'? Its bound to change under some time scale under some  
conditions, even if its mediated by a covalent link ...



On Jan 20, 2010, at 12:31, Claudine MAYER wrote:


Hi all,

We have recently solved a structure that is a crystallographic  
dimer. We
have performed UCA experiments and we observe a monomer/dimer  
distribution
in nearly equal proportion. This distribution does not change with  
protein
concentration, meaning that the two species are not in equilibrium.  
There

is no structural differences between the dimer and the monomer.

We would be interested in similar cases, eg coexistence of 2 multimers
without exchange between the 2 forms. Does somebody have any  
explanation ?


Thank you

cheers
claudine



Pr Claudine MAYER


Université Paris Diderot - Paris 7

Dynamique structurale des Macromolécules
Département de Biologie Structurale et Chimie
Institut Pasteur
25 rue du Dr Roux
75 015 PARIS
Tel. 01 45 68 83 87
Mobil. 06 07 23 51 16
Fax. 01 45 68 89 93
Mail. ma...@pasteur.fr



P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] two multmeric species in solution

[Herman . Schreuder]

Hi Claudine,

You could also look into the possibility that domain swapping occurred in half 
of your proteins. See e.g. Bennett MJ, Schlunegger MP, Eisenberg D. (1995). "3D 
domain swapping: a mechanism for oligomer assembly". Protein Sci 4 (12): 
2455-68. PMID 8580836 

Best regards,
Herman

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Claudine 
MAYER
Sent: Wednesday, January 20, 2010 12:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] two multmeric species in solution

Hi all,

We have recently solved a structure that is a crystallographic dimer. We have 
performed UCA experiments and we observe a monomer/dimer distribution in nearly 
equal proportion. This distribution does not change with protein concentration, 
meaning that the two species are not in equilibrium. There is no structural 
differences between the dimer and the monomer.

We would be interested in similar cases, eg coexistence of 2 multimers without 
exchange between the 2 forms. Does somebody have any explanation ?

Thank you

cheers
claudine



Pr Claudine MAYER


Université Paris Diderot - Paris 7

Dynamique structurale des Macromolécules Département de Biologie Structurale et 
Chimie Institut Pasteur
25 rue du Dr Roux
75 015 PARIS
Tel. 01 45 68 83 87
Mobil. 06 07 23 51 16
Fax. 01 45 68 89 93
Mail. ma...@pasteur.fr

[ccp4bb] ligand with alternate conformation?

[Kelly Daughtry]

Hello all,

I am refining a structure (using REFMAC currently, but have tried with
phenix as well) with a ligand with alternate conformations.
I have added each conformation to the pdb file with 0.5 occupancy and
named as A and B and have been able to refine that.
The problem is only two atoms are in an alternate conformation, while
I have 17 atoms total in my ligand (which are positioned the same -
i.e. a carboxyl and sugar ring I only see density for one
conformation).

After a round of refinement with A and B conformations of the entire
ligand, I have two conformations of my ligand (one shifted relative to
the other in the density) in which the second conformation does not
fit into the density, except for the 2 atoms of concern.

If I refine with just the two atoms that are different labelled as
partial occupancy A and B, a bond is broken in my main (or rather
'productive') ligand binding conformation, and  the bond remains with
the 2nd conformation.

My question is should I make a LINK in the cif file for this ligand to
restrain the bond I want to keep? Is that the best way to go about
this?

I initially tried putting both conformations of the two atoms into the
CIF file, but that is not correct as the CIF file thinks that they are
both fully there (i.e. no occupancy in the CIF file) (used
phenix.elbow to generate CIF files).

Any suggestions on how to move forward?

Thanks in advance,
Kelly


***
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
***

Re: [ccp4bb] ligand with alternate conformation?

[Herman . Schreuder]

Dear Kelly,

The way I proceed in these cases is to make a "real" alternative
conformation with the same chain ID and residue number. Example:
HETATM 1260  N1 AEPE L   1   0.875  15.892  20.141  0.50  7.15
N
HETATM 1261  N1 BEPE L   1   0.885  15.884  20.143  0.50 43.64
N
HETATM 1262  C2 AEPE L   1   1.461  16.363  21.411  0.50  7.56
C
HETATM 1263  C2 BEPE L   1   1.463  16.379  21.413  0.50 43.79
C
HETATM 1264  C3 AEPE L   1   0.517  15.990  22.572  0.50  7.83
C
HETATM 1265  C3 BEPE L   1   0.544  16.014  22.575  0.50 43.83
C

If you used two "separate" ligand molecules, this is the first thing to
try to solve the issue with the bonds. To avoid this kind of issues, I
make alternatives for all atoms of the ligand. I do not have experiences
with phenix, but in my hands in refmac there are still residual
repulsions between the alternate conformations, which as far as I know
have not yet been resolved. For this reason I switched to Buster where I
do not observe these residual repulsions.

Best regards,
Herman



-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Kelly Daughtry
Sent: Wednesday, January 20, 2010 2:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ligand with alternate conformation?

Hello all,

I am refining a structure (using REFMAC currently, but have tried with
phenix as well) with a ligand with alternate conformations.
I have added each conformation to the pdb file with 0.5 occupancy and
named as A and B and have been able to refine that.
The problem is only two atoms are in an alternate conformation, while I
have 17 atoms total in my ligand (which are positioned the same - i.e. a
carboxyl and sugar ring I only see density for one conformation).

After a round of refinement with A and B conformations of the entire
ligand, I have two conformations of my ligand (one shifted relative to
the other in the density) in which the second conformation does not fit
into the density, except for the 2 atoms of concern.

If I refine with just the two atoms that are different labelled as
partial occupancy A and B, a bond is broken in my main (or rather
'productive') ligand binding conformation, and  the bond remains with
the 2nd conformation.

My question is should I make a LINK in the cif file for this ligand to
restrain the bond I want to keep? Is that the best way to go about this?

I initially tried putting both conformations of the two atoms into the
CIF file, but that is not correct as the CIF file thinks that they are
both fully there (i.e. no occupancy in the CIF file) (used phenix.elbow
to generate CIF files).

Any suggestions on how to move forward?

Thanks in advance,
Kelly


***
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
***

[ccp4bb] DMMULTI question

[Joe Cockburn]

Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a couple of things I don't
understand.

1. You input F, SIGF, the initial best phase estimate and the Figure of
Merit. But how does DM calculate a map from this? Where does it get the
Fcalc from?

2. The program outputs the modified phases and their weights - but again,
how do you calculate a map from this?

Any help/commente would be appreciated!
Thanks
Joe

[ccp4bb] Projection of map?

[Dirk Kostrewa]

Dear CCP4ers,

I want to calculate projections of an electron density map covering a 
molecule along arbitrary directions. Please note: I don't want to 
calculate the usual centric zone projections by using (h0l) zones and 
alike, but really work on the map. Which program can I use for that?


Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] Resolution limits in refmac

[Christian Strube]

Hi ccp4bb,

I have a big problem concerning refmac_5.5.0088. I refined a couple of 
structures. Now after refining I realized that refmac sets wrong 
resolution limits for my data. Scaling was done with scala. I cut the 
data at 1.8 A. Then I used molrep; respectively difference fourier. 
Later in refmac I set 1.8A as resolution limit as well. But in the 
logfile and in the output-pdb-file there is 1.64A written as resolution 
limit. In addition the completeness is 80% instead of 98. With my other 
datasets refmac behaves similar (1.87 instead of 2.1, …). What do I have 
to do that refmac applies and doesn´t change my settings?


Thanks in advance for any advise,

Christian

Re: [ccp4bb] Projection of map?

[Leiman Petr]

> Dear CCP4ers,
> 
> I want to calculate projections of an electron density map covering a
> molecule along arbitrary directions. Please note: I don't want to
> calculate the usual centric zone projections by using (h0l) zones and
> alike, but really work on the map. Which program can I use for that?

Use one of the 3D EM software packages such as EMAN or Spider (both read in 
CCP4 maps, and EMAN even maintains pixel size and other parameters)

EMAN:
http://blake.bcm.tmc.edu/eman/eman1/progs/project3d.html

Spider:
http://www.wadsworth.org/spider_doc/spider/docs/man/pj3q.html

Best,

Petr

---
Petr Leiman
Head of the Laboratory of Structural Biology and Biophysics
Institut de physique des systèmes biologiques 
École Polytechnique Fédérale de Lausanne (EPFL)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland
Phone: +41 21 69 30441
Mobile: +41 79 538 7647
Fax:+41 21 69 30422




> 
> Best regards,
> 
> Dirk.
> 
> --
> 
> ***
> Dirk Kostrewa
> Gene Center, A 5.07
> Ludwig-Maximilians-University
> Feodor-Lynen-Str. 25
> 81377 Munich
> Germany
> Phone:+49-89-2180-76845
> Fax:  +49-89-2180-76999
> E-mail:   kostr...@genzentrum.lmu.de
> WWW:  www.genzentrum.lmu.de
> ***

[ccp4bb] bioactive glass 45S5

[cedric bauvois]

Hi everybody,

sorry for my off-topic question. We would be interested to try bioglass 45S5
in heterogeneous nucleation experiments. Does anybody know a company that
sells it?

Thank you and best regards,

Cédric Bauvois

-- 
..
Dr. Cedric Bauvois
Cristallographie des protéines
Institut de Recherches Microbiologiques J.-M. Wiame -IRMW
Campus CERIA - Av. E. Gryson, 1
B-1070 Bruxelles, BELGIUM
e-mail: cedric.bauv...@ulb.ac.be
tél: +32 (0)2 5273634
fax: +32 (0)2 5267273
..

[ccp4bb] UV microscope for screening

[Scott Walsh]

Dear CCP4BB members,

I am shopping around for a UV microscope for the lab and would like to get some 
feedback 
about peoples' experiences using UV microscopes for screening crystals.

Best,

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-

Re: [ccp4bb] problem with Coot:findwaters in ccp4i

[Paula Salgado]

Hi Tim

If I type findwaters, it finds the command without any problems. Also, Coot
directory is in the same path as in the previous version - that worked fine.
I can't see a clear reason for it not to work from within ccp4i or Refmac...

Any help is appreciated...

Paula

2010/1/20 Tim Gruene 

> Hi Paula,
>
> did you check if Coot/bin is in the PATH variable when you start ccp4i?
> Maybe the coot executable you run is a wrapper that sets the path which is
> not done as you start ccp4i.
>
> Try to type 'findwaters' from the same terminal you start ccp4i from. Does
> that yield a 'command not found'?
>
> Tim
>
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> On Tue, 19 Jan 2010, Paula Salgado wrote:
>
> > Hi everyone
> >
> > I just downloaded and installed the newest ccp4i release, including Coot
> > 0.6.0. It all seemed fine, except when I try to run refmac from ccp4i,
> > using the "Run Coot:findwaters", process fails with error message;
> >
> >
> **
> >
> > The program run with command: findwaters --pdbin
> > "/tmp/psalgado/test_pdb_1.tmp" --hklin "/tmp/psalgado/test_mtz_1.tmp" --f
> > DELFWT --phi PHDELWT --pdbout "/tmp/psalgado/test_1.tmp" --sigma 2.0
> >
> > has failed with error message
> >
> > couldn't execute "findwaters": no such file or directory
> >
> >
> ***
> >
> >
> > #CCP4I TERMINATION STATUS 0 "couldn't execute "findwaters": no such file
> > or directory"
> >
> > #CCP4I TERMINATION TIME 19 Jan 2010 12:39:26
> >
> > #CCP4I MESSAGE Task failed
> >
> >
> >
> > I checked and the Coot/bin directory exists and it contains a
> > "findwaters" executable file.
> >
> > I should add that doing "find waters" within Coot works fine.
> >
> >
> > Any ideas? All help welcomed.
> >
> >
> > Thanks!
> >
> > Paula
> >
> > =
> >
> >  Dr Paula Salgado
> >
> >  Division of Molecular Biosciences
> >  Department of Life Sciences
> >  Faculty of Natural Sciences
> >  Biochemistry Building, 5th Floor
> >  Imperial College London
> >  South Kensington Campus
> >  SW7 2AZ
> >  London
> >
> > Tel: 02075945464
> > Fax: +44 (0)20 7594 3057
> >
> >
>

Re: [ccp4bb] DMMULTI question

[Kevin Cowtan]

Joe Cockburn wrote:

Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a couple of things I don't
understand.

1. You input F, SIGF, the initial best phase estimate and the Figure of
Merit. But how does DM calculate a map from this? Where does it get the
Fcalc from?


If all you have is the 'best' phase and figure of merit, then there is a 
corresponding best estimate for Fcalc, given by


(F_calc, phi_calc) = (fom*F_obs, phi_best)

You can prove that this F_calc will produce the least noisy maps.


2. The program outputs the modified phases and their weights - but again,
how do you calculate a map from this?


Exactly the same way.

For example, in Coot, use Open MTZ (not auto), check the 'Use FOM' box 
and select the FOM. So you need to use the columns for FOBS, PHIDM and 
FOMDM.


Kevin

Re: [ccp4bb] UV microscope for screening

[Pascal Egea]

Dear Scott,

We had a UV inspection microscope from KORIMA to look at crystals by UV
fluorescence. It works relatively well but it is expensive ( way too much in
my opinion), you pay for the microscope, the UV source and the software
(named Wasabi) that comes with it
An alternative to that is described in the paper from Alan D'Arcy and coll.
Acta Cryst D63 (2007) p550-554. They use a DUVI 204 LIght source (from PLS
design GmbH , in germany) adapted to their Crystal Score system. If I
understood well, this is a just a UV source light adapted to your microscope
of choice. It is probably much cheaper and as efficient.

Hope this helps.


-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
314 Biomedical Sciences Research Building
office (310)-983-3515
lab (310)-983-3516
email pe...@mednet.ucla.edu

Re: [ccp4bb] naming convention for the guanidine group of Arginine

[Dale Tronrud]

   You are right, NH1 and NH2 are distinct in a way that CD1 and
CD2 in Phenylalanine are not, since the torsion angle that exchanges
them is not freely rotatable (except perhaps in a highly acidic
solution).

   The practical difference is that the convention for defining
labels in Phe and the others cuts the most populated region in
half.  Even for models that obey the convention you can have two
extremely similar conformations that appear very different because
the atom labels are swapped.  This means that your comparison software
has to have some way to sometimes match CD1 with CD1 in the other
side chain and other times match CD1 with CD2.  You pick the match
that gives the lowest rms difference.

   This problem should never occur in Arginine because the definition
of the labels cuts through an unpopulated region of the torsion angle
distribution.  NH1 should always be matched to NH1.

   However, I continually run into models where the labeling convention
for NH1/NH2 is violated.  You can either add an initial pass through
the models fixing the labeling when comparing models, or use the
code you all ready have to have for Phenylalanine and the like to
decide the match using rms's.

Dale Tronrud

Charlie Bond wrote:
> Hi Gerard,
> 
> Interesting - isn't it the case that for Arg, the the NH1 and NH2 atoms
> are chemically distinguishable and the convention is unambiguous (NH1
> cis to CD and NH2 trans, if I recall correctly).
> 
> The truly symmetric sidechains of Asp, Glu, Tyr, Phe, and the
> pseudosymmetric sidechains of Asn, Gln and His are more straightforward,
> but for Arg I would have thought quite a strong case would have to be
> made for ignoring the convention for RMSD purposes. Put differently, I
> find it hard to envision a scenario where swapping the names of NH1 and
> NH2 for the purposes of an RMSD would be useful. Would one also not have
> to include NE in the redundancy?
> 
> Cheers,
> Charlie
> 
> Gerard DVD Kleywegt wrote:
>>> Is there any convention to define the order of the two terminal
>>> nitrogens (NH1 and NH2) of the arginine side chain. For example,
>>> should the name NH1 be assigned to the nitrogen that is in trans
>>> position with respect to the CD carbon, and NH2 to the nitrogen in
>>> cis (or viceversa)?
>>
>> Yes there is a convention. Programs such as LSQMAN
>> (http://xray.bmc.uu.se/usf/lsqman_man.html#S32) and WhatCheck can
>> detect/fix these for you. This is something you would normally do at
>> the end of your refinement. When you compare two models using all
>> atoms, it's not so important that you use the correct convention but
>> rather the one that gives the smallest RMSD (as the atoms are
>> chemically indistinguishable). See:
>> http://xray.bmc.uu.se/usf/lsqman_man.html#S33
>>
>> --dvd
>>
>> **
>>Gerard J.  Kleywegt
>>Dept. of Cell & Molecular Biology  University of Uppsala
>>Biomedical Centre  Box 596
>>SE-751 24 Uppsala  SWEDEN
>>
>> http://xray.bmc.uu.se/gerard/  mailto:ger...@xray.bmc.uu.se
>> **
>>The opinions in this message are fictional.  Any similarity
>>to actual opinions, living or dead, is purely coincidental.
>> **
>>
> 

[ccp4bb] refmac resolution limit vs twin refine

[Christian Strube]

Hi,

I just found out, that this effect just occurs when I push the "twin 
refine" button. I have 4 slightly twinned datasets, and so far the twin 
refine worked very well...but this should not happen, I think.

Any explanations or advise?

greetings,

Christian


Hi ccp4bb,

I have a big problem concerning refmac_5.5.0088. I refined a couple of 
structures. Now after refining I realized that refmac sets wrong 
resolution limits for my data. Scaling was done with scala. I cut the 
data at 1.8 A. Then I used molrep; respectively difference fourier. 
Later in refmac I set 1.8A as resolution limit as well. But in the 
logfile and in the output-pdb-file there is 1.64A written as resolution 
limit. In addition the completeness is 80% instead of 98. With my other 
datasets refmac behaves similar (1.87 instead of 2.1, ...). What do I 
have to do that refmac applies and doesn?t change my settings?


Thanks in advance for any advise,

Christian

[ccp4bb] Refining against images instead of only reflections

[Jacob Keller]

Dear Crystallographers,

One can see from many posts on this listserve that in any given x-ray 
diffraction experiment, there are more data than merely the diffraction 
spots. Given that we now have vastly increased computational power and data 
storage capability, does it make sense to think about changing the paradigm 
for model refinements? Do we need to "reduce" data anymore? One could 
imagine applying various functions to model the intensity observed at every 
single pixel on the detector. This might be unneccesary in many cases, but 
in some cases, in which there is a lot of diffuse scattering or other 
phenomena, perhaps modelling all of the pixels would really be more true to 
the underlying phenomena? Further, it might be that the gap in R values 
between high- and low-resolution structures would be narrowed significantly, 
because we would be able to model the data, i.e., reproduce the images from 
the models, equally well for all cases. More information about the nature of 
the underlying macromolecules might really be gleaned this way. Has this 
been discussed yet?


Regards,

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] ligand with alternate conformation?

[Pavel Afonine]

Hi Kelly,

since you mentioned you tried refinement in phenix.refine:

I guess I know what the problem is, but I wouldn't tell before I'm sure. 
Could you send me the two PDB files: before and after refinement (to my 
email, not to the whole bb), and specify which residue/ligand is in 
trouble? If you send the data as well, then that would increase the 
chances of finding the solution to this -:)


Pavel.

On 1/20/10 5:33 AM, Kelly Daughtry wrote:

Hello all,

I am refining a structure (using REFMAC currently, but have tried with
phenix as well) with a ligand with alternate conformations.
I have added each conformation to the pdb file with 0.5 occupancy and
named as A and B and have been able to refine that.
The problem is only two atoms are in an alternate conformation, while
I have 17 atoms total in my ligand (which are positioned the same -
i.e. a carboxyl and sugar ring I only see density for one
conformation).

After a round of refinement with A and B conformations of the entire
ligand, I have two conformations of my ligand (one shifted relative to
the other in the density) in which the second conformation does not
fit into the density, except for the 2 atoms of concern.

If I refine with just the two atoms that are different labelled as
partial occupancy A and B, a bond is broken in my main (or rather
'productive') ligand binding conformation, and  the bond remains with
the 2nd conformation.

My question is should I make a LINK in the cif file for this ligand to
restrain the bond I want to keep? Is that the best way to go about
this?

I initially tried putting both conformations of the two atoms into the
CIF file, but that is not correct as the CIF file thinks that they are
both fully there (i.e. no occupancy in the CIF file) (used
phenix.elbow to generate CIF files).

Any suggestions on how to move forward?

Thanks in advance,
Kelly


***
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
***
  

Re: [ccp4bb] Refining against images instead of only reflections

[Bernhard Rupp]

I think these arguments for image conservation and image *use* are well
taken.
The best source of information of what is going on my be the imgCIF
people, - I'd start with Andy Howard and Herbert Bernstein.

I think that image data (after detector- and configuration-specific 
corrections to the raw images that should be quite accurate) might be
a good start for such efforts. 

I also think that this is a *most interesting area* combining X-ray physics
and
biomolecular refinement. This also kills the idea. Because the NSF will
reject 
any proposal because it has the b-word (bio) in it, and NIH will reject it 
because it has the p-word (physics) in it.
 
If someone still wants to try, let me know.

Best, BR

-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob
Keller
Sent: Wednesday, January 20, 2010 9:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refining against images instead of only reflections

Dear Crystallographers,

One can see from many posts on this listserve that in any given x-ray 
diffraction experiment, there are more data than merely the diffraction 
spots. Given that we now have vastly increased computational power and data 
storage capability, does it make sense to think about changing the paradigm 
for model refinements? Do we need to "reduce" data anymore? One could 
imagine applying various functions to model the intensity observed at every 
single pixel on the detector. This might be unneccesary in many cases, but 
in some cases, in which there is a lot of diffuse scattering or other 
phenomena, perhaps modelling all of the pixels would really be more true to 
the underlying phenomena? Further, it might be that the gap in R values 
between high- and low-resolution structures would be narrowed significantly,

because we would be able to model the data, i.e., reproduce the images from 
the models, equally well for all cases. More information about the nature of

the underlying macromolecules might really be gleaned this way. Has this 
been discussed yet?

Regards,

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Refining against images instead of only reflections

[William G. Scott]

Dear Jacob:

I think the main impediment is that more diffuse scattering, for example, isn't 
as easy to model as Bragg crystalline diffraction.  But it is definitely useful.

One example is tRNA:

http://scripts.iucr.org/cgi-bin/paper?am0009

Acta Cryst. (1994). D50, 210-218[ doi:10.1107/S0907444993011692 ]

Analysis of diffuse scattering from yeast initiator tRNA crystals

A. R. Kolatkar, J. B. Clarage and G. N. Phillips Jnr

Abstract: Yeast initiator tRNA crystals exhibit strong X-ray diffuse 
scattering. This scattering can be used to extract information about 
lattice-coupled and intramolecular motions in the crystals. The amplitudes and 
correlation distances of these motions can be estimated by calculating the 
diffuse scattering and comparing the results with the observed scattering. 
Results indicate that both anisotropic, lattice-coupled motions as well as 
short-range correlated local disorder in the anticodon arm contribute to the 
overall disorder in the crystals. These types of motions can be correlated with 
aspects of tRNA function. This additional information complements the results 
from analysis of crystallographic data and provides a more detailed picture of 
the structure and dynamics of the molecule. The degree to which the methodology 
presented here can account for the observed diffuse scattering from tRNA 
represents a significant step forward in the ability to use this conventionally 
discarded information, and encourages the ultimate extension of these ideas to 
a wide variety of macromolecular systems.


This is an example I am familiar with, but I am sure there are others.

Bill



On Jan 20, 2010, at 9:47 AM, Jacob Keller wrote:

> Dear Crystallographers,
> 
> One can see from many posts on this listserve that in any given x-ray 
> diffraction experiment, there are more data than merely the diffraction 
> spots. Given that we now have vastly increased computational power and data 
> storage capability, does it make sense to think about changing the paradigm 
> for model refinements? Do we need to "reduce" data anymore? One could imagine 
> applying various functions to model the intensity observed at every single 
> pixel on the detector. This might be unneccesary in many cases, but in some 
> cases, in which there is a lot of diffuse scattering or other phenomena, 
> perhaps modelling all of the pixels would really be more true to the 
> underlying phenomena? Further, it might be that the gap in R values between 
> high- and low-resolution structures would be narrowed significantly, because 
> we would be able to model the data, i.e., reproduce the images from the 
> models, equally well for all cases. More information about the nature of the 
> underlying macromolecules might really be gleaned this way. Has this been 
> discussed yet?
> 
> Regards,
> 
> Jacob Keller
> 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***

Re: [ccp4bb] Refining against images instead of only reflections

[Herbert J. Bernstein]

I agree with Bernhard -- both on the soundness of the idea and on 
the difficulty in finding the right home for it in NSF or NIH, but

I would suggest giving it a try. -- Herbert

=
 Herbert J. Bernstein, Professor of Computer Science
   Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769

 +1-631-244-3035
 y...@dowling.edu
=

On Wed, 20 Jan 2010, Bernhard Rupp wrote:


I think these arguments for image conservation and image *use* are well
taken.
The best source of information of what is going on my be the imgCIF
people, - I'd start with Andy Howard and Herbert Bernstein.

I think that image data (after detector- and configuration-specific
corrections to the raw images that should be quite accurate) might be
a good start for such efforts.

I also think that this is a *most interesting area* combining X-ray physics
and
biomolecular refinement. This also kills the idea. Because the NSF will
reject
any proposal because it has the b-word (bio) in it, and NIH will reject it
because it has the p-word (physics) in it.

If someone still wants to try, let me know.

Best, BR

-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob
Keller
Sent: Wednesday, January 20, 2010 9:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refining against images instead of only reflections

Dear Crystallographers,

One can see from many posts on this listserve that in any given x-ray
diffraction experiment, there are more data than merely the diffraction
spots. Given that we now have vastly increased computational power and data
storage capability, does it make sense to think about changing the paradigm
for model refinements? Do we need to "reduce" data anymore? One could
imagine applying various functions to model the intensity observed at every
single pixel on the detector. This might be unneccesary in many cases, but
in some cases, in which there is a lot of diffuse scattering or other
phenomena, perhaps modelling all of the pixels would really be more true to
the underlying phenomena? Further, it might be that the gap in R values
between high- and low-resolution structures would be narrowed significantly,

because we would be able to model the data, i.e., reproduce the images from
the models, equally well for all cases. More information about the nature of

the underlying macromolecules might really be gleaned this way. Has this
been discussed yet?

Regards,

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] UV microscope for screening

[Gabriel Birrane]

I received this in the mail today. You may be interested.

http://www.fmpproducts.com

They have products for crystallography


On Wed, 2010-01-20 at 11:28 -0500, Scott Walsh wrote:
> Dear CCP4BB members,
> 
> I am shopping around for a UV microscope for the lab and would like to get 
> some feedback 
> about peoples' experiences using UV microscopes for screening crystals.
> 
> Best,
> 
> 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-
> 

[ccp4bb] FW: [ccp4bb] Refining against images instead of only reflections

[Colin Nave]

 
Jacob
Yes, discussions have taken place but perhaps more private than on the
CCP4 bulleting board! So I am glad someone has raised the issue.

The present approximation that people make works very well in the
majority of cases. The approximation is implied during the integration
of a spot and is that the crystal consists of an infinite number of
identical unit cells (same contents and lattice repeats). I have
jokingly "blamed" Bragg for this approximation but James Holton has
pointed out that he also derived the "minimum wavelength principle" so
was fully aware of continuous transforms etc.

With significant different conformations in the unit cells, different
lattice constants, lattice couplings, strain, misaligned domains etc.
both complex spot profiles and diffuse scatter will result. By modeling
this properly (e.g. a proper model of crystal plus its contents and the
effects on the diffraction pattern) one should be able to get more
information. Measurements of the 3D shape of the Bragg peaks (ideally in
the near and far fields!) plus the diffuse scatter near and far from the
Bragg peaks would be ideal. A parallel beam and high resolution
detectors would be required to do this properly i.e. a similar set up to
that used for topographic studies (e.g. Lovelace and Borgstahl work plus
of course many other investigators). I think much of this was undertaken
as a method to monitor improvements in crystal growth rather than get
better diffraction data but the model of the crystal should be
applicable to obtaining better data for structure determination.  At the
moment this is too ambitious but, a lower resolution model of the
crystal could still be obtained with standard set ups and used in a
variety of ways.

Coincidently, I am involved at the moment on a beamline with a project
to obtain high resolution images of diffraction spots using a coherent
beam. Small molecule crystals at the moment but my motivation is to
extend to protein crystals. Don't know whether will ever get there
though.

So yes, plenty to discuss but doing something is a lot harder! 

I have only mentioned using such data. Making it available is another
issue, as others have said.

Regards
  Colin


 

> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of 
> Jacob Keller
> Sent: 20 January 2010 17:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refining against images instead of only reflections
> 
> Dear Crystallographers,
> 
> One can see from many posts on this listserve that in any given x-ray 
> diffraction experiment, there are more data than merely the 
> diffraction spots. Given that we now have vastly increased 
> computational power and data storage capability, does it make sense to

> think about changing the paradigm for model refinements? Do we need to

> "reduce" data anymore? One could imagine applying various functions to

> model the intensity observed at every single pixel on the detector.
> This might be unneccesary in many cases, but in some cases, in which 
> there is a lot of diffuse scattering or other phenomena, perhaps 
> modelling all of the pixels would really be more true to the 
> underlying phenomena? Further, it might be that the gap in R values 
> between high- and low-resolution structures would be narrowed 
> significantly, because we would be able to model the data, i.e., 
> reproduce the images from the models, equally well for all cases. More

> information about the nature of the underlying macromolecules might 
> really be gleaned this way. Has this been discussed yet?
> 
> Regards,
> 
> Jacob Keller
> 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***
> 

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Re: [ccp4bb] refmac resolution limit vs twin refine

[Garib Murshudov]

I thought this problem is fixed. Could you please try the version from:

www.ysbl.york.ac.uk/refmac/latest_refmac.html

Problem was that when refmac starts twinning analysis it uses generous  
tolerance and then filters out unlikely twin operators.
When large deformation is needed merohedral twinning to occur then  
resolution of twin mates may be different.
In the version you are working refmac forgets to recalculate  
resolution. In the version from above web site it should be corrected.


regards
Garib

On 20 Jan 2010, at 17:22, Christian Strube wrote:


Hi,

I just found out, that this effect just occurs when I push the "twin  
refine" button. I have 4 slightly twinned datasets, and so far the  
twin refine worked very well...but this should not happen, I think.

Any explanations or advise?

greetings,

Christian


Hi ccp4bb,

I have a big problem concerning refmac_5.5.0088. I refined a couple  
of structures. Now after refining I realized that refmac sets wrong  
resolution limits for my data. Scaling was done with scala. I cut  
the data at 1.8 A. Then I used molrep; respectively difference  
fourier. Later in refmac I set 1.8A as resolution limit as well. But  
in the logfile and in the output-pdb-file there is 1.64A written as  
resolution limit. In addition the completeness is 80% instead of 98.  
With my other datasets refmac behaves similar (1.87 instead of  
2.1, ...). What do I have to do that refmac applies and doesn?t  
change my settings?


Thanks in advance for any advise,

Christian

Re: [ccp4bb] UV microscope for screening

[Phoebe Rice]

Are these things really cost-effective?  That is, compared to
the cost of simply posting a list of evil salts like Mg
ammonium phosphate on the wall and testing a few duds in the
x-ray beam?
  Phoebe

 Original message 
>Date: Wed, 20 Jan 2010 13:59:23 -0500
>From: Gabriel Birrane   
>Subject: Re: [ccp4bb] UV microscope for screening  
>To: CCP4BB@JISCMAIL.AC.UK
>
>I received this in the mail today. You may be interested.
>
>http://www.fmpproducts.com
>
>They have products for crystallography
>
>
>On Wed, 2010-01-20 at 11:28 -0500, Scott Walsh wrote:
>> Dear CCP4BB members,
>> 
>> I am shopping around for a UV microscope for the lab and
would like to get some feedback 
>> about peoples' experiences using UV microscopes for
screening crystals.
>> 
>> Best,
>> 
>> 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-
>> 
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them 
  both in one book
Please do take a 
  really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp

Re: [ccp4bb] Refining against images instead of only reflections

[Paul Smith]

Hi Jacob,

I see you're still in the crystallography business.

While you have an interesting idea, I doubt refining structures against entire 
images would be of any use in obtaining higher quality macromolecular 
structures.  Much of what you see on the screen is a function of parameters 
completely unrelated or irrelevant to the structure being studied.  Diffuse 
scattering can come from the cryo liquid surrounding the crystal as well as the 
fibers of the mounting loop itself.  Background scattering is related to beam 
collimation.  Spot size/shape is a function of crystal morphology among other 
things.  In addition, every detector has its own peculiarities that make the 
intensities observed apart from diffraction spots particular to that detector.  
Also, you would have to take into account other physical properties such as 
ambient temperature, detector dark current fluctuations, variations in air 
absorption, etc.

So, you could conceivably fit all of these various parameters to the images on 
hand, but none of them give  you any actual information about your structure.  
As always, if you want more information about your structure, get higher 
resolution data.

Nonetheless, I do think some thought could be put in to exactly how data are 
reduced.  Perhaps the impending era of real time detector readout will help us 
rethink about spot profiles and intensity integration in a more sophisticated 
way. We may see a return to thinking about ccd readouts like an area detector 
which makes the process of analyzing images moot.

--Paul

--- On Wed, 1/20/10, Jacob Keller  wrote:

> From: Jacob Keller 
> Subject: [ccp4bb] Refining against images instead of only reflections
> To: CCP4BB@JISCMAIL.AC.UK
> Date: Wednesday, January 20, 2010, 12:47 PM
> Dear Crystallographers,
> 
> One can see from many posts on this listserve that in any
> given x-ray diffraction experiment, there are more data than
> merely the diffraction spots. Given that we now have vastly
> increased computational power and data storage capability,
> does it make sense to think about changing the paradigm for
> model refinements? Do we need to "reduce" data anymore? One
> could imagine applying various functions to model the
> intensity observed at every single pixel on the detector.
> This might be unneccesary in many cases, but in some cases,
> in which there is a lot of diffuse scattering or other
> phenomena, perhaps modelling all of the pixels would really
> be more true to the underlying phenomena? Further, it might
> be that the gap in R values between high- and low-resolution
> structures would be narrowed significantly, because we would
> be able to model the data, i.e., reproduce the images from
> the models, equally well for all cases. More information
> about the nature of the underlying macromolecules might
> really be gleaned this way. Has this been discussed yet?
> 
> Regards,
> 
> Jacob Keller
> 
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> ***
> 

Re: [ccp4bb] UV microscope for screening

[Ed Pozharski]

Phoebe,

my understanding is that power of UV illumination here is not in
salt-vs-protein test (which, imho, can only be finalized by testing
diffraction) but in improved contrast for protein crystal detection.  I
haven't used UV microscopes myself, but images provided by manufacturers
are quite impressive
http://www.rigaku.com/images/automation/uv-before.jpg
http://www.rigaku.com/images/automation/uv-after.jpg

Of course, these images are advertisement and may be exaggerated.

On the salt/protein issue, I wholeheartedly agree.

Ed.

On Wed, 2010-01-20 at 13:52 -0600, Phoebe Rice wrote:
> Are these things really cost-effective?  That is, compared to
> the cost of simply posting a list of evil salts like Mg
> ammonium phosphate on the wall and testing a few duds in the
> x-ray beam?
>   Phoebe
> 
>  Original message 
> >Date: Wed, 20 Jan 2010 13:59:23 -0500
> >From: Gabriel Birrane   
> >Subject: Re: [ccp4bb] UV microscope for screening  
> >To: CCP4BB@JISCMAIL.AC.UK
> >
> >I received this in the mail today. You may be interested.
> >
> >http://www.fmpproducts.com
> >
> >They have products for crystallography
> >
> >
> >On Wed, 2010-01-20 at 11:28 -0500, Scott Walsh wrote:
> >> Dear CCP4BB members,
> >> 
> >> I am shopping around for a UV microscope for the lab and
> would like to get some feedback 
> >> about peoples' experiences using UV microscopes for
> screening crystals.
> >> 
> >> Best,
> >> 
> >> 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-
> >> 
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> 
> RNA is really nifty
> DNA is over fifty
> We have put them 
>   both in one book
> Please do take a 
>   really good look
> http://www.rsc.org/shop/books/2008/9780854042722.asp


-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

Re: [ccp4bb] Refining against images instead of only reflections

[Soisson, Stephen M]

Jacob-

Based on your question, you would likely be interested in doing some
literature searches for the pioneering work of George Phillips and the
utilization of diffuse scattering information.  What you are thinking
about has already been broached - nearly 20 yrs ago.  It is likely that
a revisitation of this topic could be fruitful in certain cases.

Best regards,

Steve 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jacob Keller
Sent: Wednesday, January 20, 2010 12:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refining against images instead of only reflections

Dear Crystallographers,

One can see from many posts on this listserve that in any given x-ray 
diffraction experiment, there are more data than merely the diffraction 
spots. Given that we now have vastly increased computational power and
data 
storage capability, does it make sense to think about changing the
paradigm 
for model refinements? Do we need to "reduce" data anymore? One could 
imagine applying various functions to model the intensity observed at
every 
single pixel on the detector. This might be unneccesary in many cases,
but 
in some cases, in which there is a lot of diffuse scattering or other 
phenomena, perhaps modelling all of the pixels would really be more true
to 
the underlying phenomena? Further, it might be that the gap in R values 
between high- and low-resolution structures would be narrowed
significantly, 
because we would be able to model the data, i.e., reproduce the images
from 
the models, equally well for all cases. More information about the
nature of 
the underlying macromolecules might really be gleaned this way. Has this

been discussed yet?

Regards,

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
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Re: [ccp4bb] Refining against images instead of only reflections

[Edward Snell]

Hi Paul,

I'll probably open myself up to criticism (welcomed) but I think I'd disagree 
with this somewhat. While crystallography from the Bragg reflections provides a 
nice static picture of the structure, looking at the diffuse scatter in more 
detail may give more knowledge about mechanism - i.e. if there are any 
characteristic modes associated with significant motion etc. Higher resolution 
is not always good, one of my enlightening experiences came from paying 
attention to collecting very complete, very low resolution data. Similarly, 
after collecting 0.8A data from a large protein I leant a lot about data 
processing but even more about how to not tell anyone, move the detector back, 
and then attenuate the beam :) The high-res provided a lot more work and didn't 
provide any more useful structural knowledge than a 1.2A data set collected in 
a fraction of the time. However, it did provide a window into how X-rays can 
perturb the structure - being greedy is not always good. 

Diffuse scattering has been neglected in the field (for good reason) but I 
think we have the processing power to take advantage of it now. To misquote 
Richard Feynman, "there is plenty of room at the bottom", make sure you get the 
low resolution information as well as the high.

I do agree that we may have to rethink image storage somewhat. Looking over a 
paper not too long ago that had over 30,000 images involved in the analysis 
made me remember the days when the tape drives were slower writing data than 
the detectors producing it. That mad scramble to start backup before starting 
collection ;) Realtime readout, continuous rotation etc., may need to redefine 
our thoughts of images.

Cheers,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660 
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu  
Telepathy: 42.2 GHz

Heisenberg was probably here!


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Smith
Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only reflections

Hi Jacob,

I see you're still in the crystallography business.

While you have an interesting idea, I doubt refining structures against entire 
images would be of any use in obtaining higher quality macromolecular 
structures.  Much of what you see on the screen is a function of parameters 
completely unrelated or irrelevant to the structure being studied.  Diffuse 
scattering can come from the cryo liquid surrounding the crystal as well as the 
fibers of the mounting loop itself.  Background scattering is related to beam 
collimation.  Spot size/shape is a function of crystal morphology among other 
things.  In addition, every detector has its own peculiarities that make the 
intensities observed apart from diffraction spots particular to that detector.  
Also, you would have to take into account other physical properties such as 
ambient temperature, detector dark current fluctuations, variations in air 
absorption, etc.

So, you could conceivably fit all of these various parameters to the images on 
hand, but none of them give  you any actual information about your structure.  
As always, if you want more information about your structure, get higher 
resolution data.

Nonetheless, I do think some thought could be put in to exactly how data are 
reduced.  Perhaps the impending era of real time detector readout will help us 
rethink about spot profiles and intensity integration in a more sophisticated 
way. We may see a return to thinking about ccd readouts like an area detector 
which makes the process of analyzing images moot.

--Paul

--- On Wed, 1/20/10, Jacob Keller  wrote:

> From: Jacob Keller 
> Subject: [ccp4bb] Refining against images instead of only reflections
> To: CCP4BB@JISCMAIL.AC.UK
> Date: Wednesday, January 20, 2010, 12:47 PM
> Dear Crystallographers,
> 
> One can see from many posts on this listserve that in any
> given x-ray diffraction experiment, there are more data than
> merely the diffraction spots. Given that we now have vastly
> increased computational power and data storage capability,
> does it make sense to think about changing the paradigm for
> model refinements? Do we need to "reduce" data anymore? One
> could imagine applying various functions to model the
> intensity observed at every single pixel on the detector.
> This might be unneccesary in many cases, but in some cases,
> in which there is a lot of diffuse scattering or other
> phenomena, perhaps modelling all of the pixels would really
> be more true to the underlying phenomena? Further, it might
> be that the gap in R values between high- and low-resolution
> structures would be narrowed significantly, because we would
> be able to mode

Re: [ccp4bb] Refining against images instead of only reflections

[Jacob Keller]

There was a thread a while back which related to this a bit:

"Re: [ccp4bb] Small lines in diffraction pattern (more info)"

In that thread, there were mentioned the papers:

Faure et al NSB 2 Feb 1994
Kajiwara J. Appl. Cryst. (1971). 4, 329

These seem to bear on the issue of diffuse scattering, and in particular the 
procedure in the NSB paper could in principle be applied to model 
refinements, I think.


Jacob


***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - 
From: "Edward Snell" 

To: 
Sent: Wednesday, January 20, 2010 2:29 PM
Subject: Re: [ccp4bb] Refining against images instead of only reflections


Hi Paul,

I'll probably open myself up to criticism (welcomed) but I think I'd 
disagree with this somewhat. While crystallography from the Bragg 
reflections provides a nice static picture of the structure, looking at the 
diffuse scatter in more detail may give more knowledge about mechanism - 
i.e. if there are any characteristic modes associated with significant 
motion etc. Higher resolution is not always good, one of my enlightening 
experiences came from paying attention to collecting very complete, very low 
resolution data. Similarly, after collecting 0.8A data from a large protein 
I leant a lot about data processing but even more about how to not tell 
anyone, move the detector back, and then attenuate the beam :) The high-res 
provided a lot more work and didn't provide any more useful structural 
knowledge than a 1.2A data set collected in a fraction of the time. However, 
it did provide a window into how X-rays can perturb the structure - being 
greedy is not always good.


Diffuse scattering has been neglected in the field (for good reason) but I 
think we have the processing power to take advantage of it now. To misquote 
Richard Feynman, "there is plenty of room at the bottom", make sure you get 
the low resolution information as well as the high.


I do agree that we may have to rethink image storage somewhat. Looking over 
a paper not too long ago that had over 30,000 images involved in the 
analysis made me remember the days when the tape drives were slower writing 
data than the detectors producing it. That mad scramble to start backup 
before starting collection ;) Realtime readout, continuous rotation etc., 
may need to redefine our thoughts of images.


Cheers,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul 
Smith

Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only reflections

Hi Jacob,

I see you're still in the crystallography business.

While you have an interesting idea, I doubt refining structures against 
entire images would be of any use in obtaining higher quality macromolecular 
structures.  Much of what you see on the screen is a function of parameters 
completely unrelated or irrelevant to the structure being studied.  Diffuse 
scattering can come from the cryo liquid surrounding the crystal as well as 
the fibers of the mounting loop itself.  Background scattering is related to 
beam collimation.  Spot size/shape is a function of crystal morphology among 
other things.  In addition, every detector has its own peculiarities that 
make the intensities observed apart from diffraction spots particular to 
that detector.  Also, you would have to take into account other physical 
properties such as ambient temperature, detector dark current fluctuations, 
variations in air absorption, etc.


So, you could conceivably fit all of these various parameters to the images 
on hand, but none of them give  you any actual information about your 
structure.  As always, if you want more information about your structure, 
get higher resolution data.


Nonetheless, I do think some thought could be put in to exactly how data are 
reduced.  Perhaps the impending era of real time detector readout will help 
us rethink about spot profiles and intensity integration in a more 
sophisticated way. We may see a return to thinking about ccd readouts like 
an area detector which makes the process of analyzing images moot.


--Paul

--- On Wed, 1/20/10, Jacob Keller  wrote:


From: Jacob Keller 
Subject: [ccp4bb] Refining against images instead of only reflections
To: CCP4BB@JISCMAIL.AC.UK
Date: Wednesday, January 20, 2010, 12:47 PM
Dear Crys

Re: [ccp4bb] Refining against images instead of only reflections

[Klaus Fütterer]

A long time ago I did a bit of Rietveld refinement and I see some  
similarities between this approach and what people have been  
proposing in this thread. Refining against the profile of the 1-d  
powder diffraction pattern rather than extracting integrated  
intensities helped to improve the quality of the refined structures  
significantly. Finding the correct (or best) profile function,  
however, took a while, at least for the X-ray case.


Klaus

===

Klaus Fütterer, Ph.D.
Reader in Structural Biology

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: k.futte...@bham.ac.uk
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/klaus/
===





On 20 Jan 2010, at 20:29, Edward Snell wrote:


Hi Paul,

I'll probably open myself up to criticism (welcomed) but I think  
I'd disagree with this somewhat. While crystallography from the  
Bragg reflections provides a nice static picture of the structure,  
looking at the diffuse scatter in more detail may give more  
knowledge about mechanism - i.e. if there are any characteristic  
modes associated with significant motion etc. Higher resolution is  
not always good, one of my enlightening experiences came from  
paying attention to collecting very complete, very low resolution  
data. Similarly, after collecting 0.8A data from a large protein I  
leant a lot about data processing but even more about how to not  
tell anyone, move the detector back, and then attenuate the beam :)  
The high-res provided a lot more work and didn't provide any more  
useful structural knowledge than a 1.2A data set collected in a  
fraction of the time. However, it did provide a window into how X- 
rays can perturb the structure - being greedy is not always good.


Diffuse scattering has been neglected in the field (for good  
reason) but I think we have the processing power to take advantage  
of it now. To misquote Richard Feynman, "there is plenty of room at  
the bottom", make sure you get the low resolution information as  
well as the high.


I do agree that we may have to rethink image storage somewhat.  
Looking over a paper not too long ago that had over 30,000 images  
involved in the analysis made me remember the days when the tape  
drives were slower writing data than the detectors producing it.  
That mad scramble to start backup before starting collection ;)  
Realtime readout, continuous rotation etc., may need to redefine  
our thoughts of images.


Cheers,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf  
Of Paul Smith

Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only  
reflections


Hi Jacob,

I see you're still in the crystallography business.

While you have an interesting idea, I doubt refining structures  
against entire images would be of any use in obtaining higher  
quality macromolecular structures.  Much of what you see on the  
screen is a function of parameters completely unrelated or  
irrelevant to the structure being studied.  Diffuse scattering can  
come from the cryo liquid surrounding the crystal as well as the  
fibers of the mounting loop itself.  Background scattering is  
related to beam collimation.  Spot size/shape is a function of  
crystal morphology among other things.  In addition, every detector  
has its own peculiarities that make the intensities observed apart  
from diffraction spots particular to that detector.  Also, you  
would have to take into account other physical properties such as  
ambient temperature, detector dark current fluctuations, variations  
in air absorption, etc.


So, you could conceivably fit all of these various parameters to  
the images on hand, but none of them give  you any actual  
information about your structure.  As always, if you want more  
information about your structure, get higher resolution data.


Nonetheless, I do think some thought could be put in to exactly how  
data are reduced.  Perhaps the impending era of real time detector  
readout will help us rethink about spot profiles and intensity  
integration in a more sophisticated way. We may see a return to  
thinking about ccd readouts like an area detector which makes the  
process of analyzing images moot.


--Paul

--- On Wed, 1/20/10, Jacob Keller   
wrote:



From: Jacob Ke

Re: [ccp4bb] Refining against images instead of only reflections

[Harry]

Hi

I, too, was struck by the potential similarity with Rietveld  
refinement, then started to think about the differences. The biggest  
difference, of course, is refining against "many" two-dimensional  
images compared to refining against a linear plot - so I'd guess in  
principle you'd get a big benefit in increasing the data:parameter  
ratio.


Of course, there's a hint above in the "refinement" part of the  
process; you need the structure and a model for the causes of the  
diffuse scatter etc to have something to refine against, so it may  
still be worthwhile extracting the Bragg intensities first to solve  
your structure.


(I've never done Rietveld refinement, but read a good book on the  
topic a few years ago -  "The Riteveld Method" ed R.A. Young. It might  
be a little out of date now...)



On 20 Jan 2010, at 21:14, Klaus Fütterer wrote:

A long time ago I did a bit of Rietveld refinement and I see some  
similarities between this approach and what people have been  
proposing in this thread. Refining against the profile of the 1-d  
powder diffraction pattern rather than extracting integrated  
intensities helped to improve the quality of the refined structures  
significantly. Finding the correct (or best) profile function,  
however, took a while, at least for the X-ray case.


Klaus

= 
==


   Klaus Fütterer, Ph.D.
   Reader in Structural Biology

School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham  F: +44-(0)-121-414 5925
Edgbaston E: k.futte...@bham.ac.uk
Birmingham, B15 2TT, UK   W: www.biochemistry.bham.ac.uk/ 
klaus/
= 
==






On 20 Jan 2010, at 20:29, Edward Snell wrote:


Hi Paul,

I'll probably open myself up to criticism (welcomed) but I think  
I'd disagree with this somewhat. While crystallography from the  
Bragg reflections provides a nice static picture of the structure,  
looking at the diffuse scatter in more detail may give more  
knowledge about mechanism - i.e. if there are any characteristic  
modes associated with significant motion etc. Higher resolution is  
not always good, one of my enlightening experiences came from  
paying attention to collecting very complete, very low resolution  
data. Similarly, after collecting 0.8A data from a large protein I  
leant a lot about data processing but even more about how to not  
tell anyone, move the detector back, and then attenuate the beam :)  
The high-res provided a lot more work and didn't provide any more  
useful structural knowledge than a 1.2A data set collected in a  
fraction of the time. However, it did provide a window into how X- 
rays can perturb the structure - being greedy is not always good.


Diffuse scattering has been neglected in the field (for good  
reason) but I think we have the processing power to take advantage  
of it now. To misquote Richard Feynman, "there is plenty of room at  
the bottom", make sure you get the low resolution information as  
well as the high.


I do agree that we may have to rethink image storage somewhat.  
Looking over a paper not too long ago that had over 30,000 images  
involved in the analysis made me remember the days when the tape  
drives were slower writing data than the detectors producing it.  
That mad scramble to start backup before starting collection ;)  
Realtime readout, continuous rotation etc., may need to redefine  
our thoughts of images.


Cheers,

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf  
Of Paul Smith

Sent: Wednesday, January 20, 2010 3:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refining against images instead of only  
reflections


Hi Jacob,

I see you're still in the crystallography business.

While you have an interesting idea, I doubt refining structures  
against entire images would be of any use in obtaining higher  
quality macromolecular structures.  Much of what you see on the  
screen is a function of parameters completely unrelated or  
irrelevant to the structure being studied.  Diffuse scattering can  
come from the cryo liquid surrounding the crystal as well as the  
fibers of the mounting loop itself.  Background scattering is  
related to beam collimation.  Spot size/shape is a function of  
crystal morphology among other things.  In addition, every detector  
has its own peculiarities that make the intensities observed apart  
from diffraction spots particular to that detector.

[ccp4bb] Acta E

[Bernhard Rupp]

I suppose most have read the Acta D editorial already
http://journals.iucr.org/d/issues/2010/01/00/me0408/me0408.pdf
but it seems another creative way of structure generation 
has been discovered by some small molecule people:
http://journals.iucr.org/e/issues/2010/01/00/me0406/me0406.pdf

Best, BR

-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@qedlife.com
bernhardr...@sbcglobal.net 
http://www.ruppweb.org/ 
-
The hard part about playing chicken
is to know when to flinch
-

[ccp4bb] convert sdf to pdf file

[Raja Dey]

Dear Friends,
 Is there anyone know how to convert sdf file into pdf 
file? sdf file contains chemdraw of a number of small molecule compounds plus 
some other parameters in different columns. I got  a source code for 
'sdf2mol.java', but is not working. Any suggestion is appreciated.
Thanks...
Raja


  The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. 
http://in.yahoo.com/

[ccp4bb] Data processing webinars

[Angela Criswell]

I would like to draw your attention to an upcoming free webinar series 
that will cover several of the most widely used X-ray diffraction data 
processing packages. This series is part of a larger webinar program that 
focuses on topics 'near and dear' to the crystallographic community. 

The first webinar in this series will take place on January 21st, 2010 at 
9:00 AM EST and will cover HKL. You can find more information and register 
for these webinars at the following site: 
http://www.rigaku.com/protein/webinars.html. 

We plan to cover a different software package each month from now until 
April or May, based on the availability of the various software authors 
and experts. The primary goal for this series is to teach users how to use 
the different data processing packages and interpret results. As we 
receive additional date and time commitments we will update the above web 
page to include additional registration links.

Best regards,
Angela



--
Angela R. Criswell, Ph. D.
Rigaku Americas Corporation
9009 New Trails Drive
The Woodlands, TX  77381
Ph: +1 281 362 2300 ext. 216
Fax: +1 281 364 3628
Email: angela.crisw...@rigaku.com
URL: http://www.Rigaku.com

Re: [ccp4bb] convert sdf to pdf file

[Andrew Orry]

Raja

You can convert sdf format to pdf via the free ICM-Browser. Download it 
here:

http://www.molsoft.com/icm_browser.html

-- read in the sdf file into ICM-Browser and it will be displayed as 
chemical spreadsheet
-- choose export to Excel and then save as PDF or use the print to file 
option in the ICM-Browser


Regards,

--
Andrew Orry Ph.D.
Senior Research Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla
CA 92037
Tel: 858-625-2000 x108
Fax: 828-625-2888


On 1/20/2010 3:14 PM, Raja Dey wrote:

Dear Friends,
 Is there anyone know how to convert sdf file into 
pdf file? sdf file contains chemdraw of a number of small molecule 
compounds plus some other parameters in different columns. I got  a 
source code for 'sdf2mol.java', but is not working. Any suggestion is 
appreciated.

Thanks...
Raja


The INTERNET now has a personality. YOURS! See your Yahoo! Homepage 
.

Re: [ccp4bb] Data processing webinars - correction

[Angela Criswell]

Please note a correction in the time zone. The correct time for the 
webinar is 9:00 AM CST so that would be 10:00 AM EST (15:00 UTC/GMT).

Angela





Angela Criswell  
Sent by: CCP4 bulletin board 
01/20/2010 05:29 PM
Please respond to
Angela Criswell 


To
CCP4BB@JISCMAIL.AC.UK
cc

Subject
[ccp4bb] Data processing webinars








I would like to draw your attention to an upcoming free webinar series 
that will cover several of the most widely used X-ray diffraction data 
processing packages. This series is part of a larger webinar program that 
focuses on topics 'near and dear' to the crystallographic community. 

The first webinar in this series will take place on January 21st, 2010 at 
9:00 AM EST and will cover HKL. You can find more information and register 
for these webinars at the following site: 
http://www.rigaku.com/protein/webinars.html. 

We plan to cover a different software package each month from now until 
April or May, based on the availability of the various software authors 
and experts. The primary goal for this series is to teach users how to use 
the different data processing packages and interpret results. As we 
receive additional date and time commitments we will update the above web 
page to include additional registration links. 

Best regards, 
Angela 



--
Angela R. Criswell, Ph. D.
Rigaku Americas Corporation
9009 New Trails Drive
The Woodlands, TX  77381
Ph: +1 281 362 2300 ext. 216
Fax: +1 281 364 3628
Email: angela.crisw...@rigaku.com
URL: http://www.Rigaku.com

[ccp4bb] XDS with CCP4i/XIA2

[SAKAMOTO Yasumitsu]

Dear all,

I am trying to process some data. When I try to run XDS through XIA2/CCP4i,
it gives an error message was descrived as below.

Status: error "XDS version "December 28, 2009" not supported"

I am using CCP4 6.1.2, XIA2 0.3.1.0 and XDS December 28,2009 with the
CCP4 Interface version 2.0.5 running on CentOS version 4.8.
Does anyone know how to solve or avoid this error.
I appreciate any advice.

Yasumitsu
-- 
SAKAMOTO Yasumitsu
Iwate Medical University
E-mail: ysaka...@iwate-med.ac.jp

Re: [ccp4bb] XDS with CCP4i/XIA2

[Nobuo OKAZAKI]

Sakamoto-san,

According to XIA2 blog, the new XDS works just fine with XIA2.
http://xia2.blogspot.com/2010/01/happy-new-xds.html

Modify value of supported_versions at line 77 in $XIA2_ROOT/Wrappers/XDS/XDS.py
   supported_versions = ['January 30, 2009']
to
   supported_versions = ['December 28, 2009']

It will make XIA2 working well.

Nobuo OKAZAKI

> Dear all,
> 
> I am trying to process some data. When I try to run XDS through XIA2/CCP4i,
> it gives an error message was descrived as below.
> 
> Status: error "XDS version "December 28, 2009" not supported"
> 
> I am using CCP4 6.1.2, XIA2 0.3.1.0 and XDS December 28,2009 with the
> CCP4 Interface version 2.0.5 running on CentOS version 4.8.
> Does anyone know how to solve or avoid this error.
> I appreciate any advice.
> 
> Yasumitsu
> -- 
> SAKAMOTO Yasumitsu
> Iwate Medical University
> E-mail: ysaka...@iwate-med.ac.jp