Re: [ccp4bb] Finding NCS operator from one heavy atom site?

[Eleanor Dodson]

I guess you mean you have one ha per monomer?

To use CCP4 tools - you can use mapmask to mask out a sphere of density 
around your heavy atom.
Give the atom a "radius" of 10A of something big to get a decent lump, 
and make sure it looks sensible..

(Use your best phases here of course)

Then use that density as your search model for MOLREP - you can see how 
to do that from the GUI I think..
(Make sure the matrices DO transform your ha in mol 1 to the ha sites in 
the other molecules!


Then input the matrices you get into DM with the averaging option - 
that will refine the rotation matrices, and usually improves the maps 
greatly.


Eleanor




Partha Chakrabarti wrote:

Hi,

Apologies for a non CCP4 question in strict sense. I am trying to work
out the NCS operators for a three wavelength
Se-MAD data which has only one site. The map is hardly interpretable.
I came across the USF Rave package and what I am aiming is

creak a mask around the heavy atom site (found by SHELX or Solve)
using mama or so, (ideally from resolve.mtz but not necessarily),

translate it to the other heavy atom site(s),
give a 6d search with NCS6d and
perhaps refine the best CC a bit with imp.

If it works, I could try use the NCS operator in DM or Resolve etc.

I was wondering if someone has a C-shell scripts for dealing with such
situation already. Of course if there are other programs for such a
task within CCP4, could give it a try.

Best Regards,
Partha


  

[ccp4bb] Pointless Error.

[David Briggs]

Morning all...

I've just downloaded the newest version of pointless, 1.2.15, using
the mac osx intel binary.

When I try and run it through the gui, it seems that my child gets hit
by some sort of bus error:


***
* Information from CCP4Interface script
***
The program run with command: pointless
has failed with error message
child killed: bus error
***


#CCP4I TERMINATION STATUS 0 "child killed: bus error"
#CCP4I TERMINATION TIME 23 May 2008  10:04:00
#CCP4I MESSAGE Task failed

If I try and run it from the command line, I just get a bus error - my
child escapes unscathed this time - even if I just type pointless
without any commands...

I'm using mac osX 10.4.11, and an intel powered machine.

Has anybody got any fixes or suggestions for this?

Cheers,

Dave

-- 

David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile

Re: [ccp4bb] Pointless Error.

[Winter, G (Graeme)]

Hi Dave,

I have been using 1.2.16 on this platform for a long while now and it is
working fine - take a look at the MRC ftp site to see if you can get the
same binary:

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre

Cheers,

Graeme 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
David Briggs
Sent: 23 May 2008 10:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Pointless Error.

Morning all...

I've just downloaded the newest version of pointless, 1.2.15, using the
mac osx intel binary.

When I try and run it through the gui, it seems that my child gets hit
by some sort of bus error:



***
* Information from CCP4Interface script

***
The program run with command: pointless
has failed with error message
child killed: bus error

***


#CCP4I TERMINATION STATUS 0 "child killed: bus error"
#CCP4I TERMINATION TIME 23 May 2008  10:04:00 #CCP4I MESSAGE Task failed

If I try and run it from the command line, I just get a bus error - my
child escapes unscathed this time - even if I just type pointless
without any commands...

I'm using mac osX 10.4.11, and an intel powered machine.

Has anybody got any fixes or suggestions for this?

Cheers,

Dave

--

David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile

Re: [ccp4bb] Pointless Error.

[David Briggs]

Thanks Graeme,

I tried 1.2.16, and got the same problem - the most recent version I
can get to work is 1.2.10 - everything after that fails.

Cheers,

Dave

2008/5/23 Winter, G (Graeme) <[EMAIL PROTECTED]>:
> Hi Dave,
>
> I have been using 1.2.16 on this platform for a long while now and it is
> working fine - take a look at the MRC ftp site to see if you can get the
> same binary:
>
> ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
>
> Cheers,
>
> Graeme
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
> David Briggs
> Sent: 23 May 2008 10:13
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Pointless Error.
>
> Morning all...
>
> I've just downloaded the newest version of pointless, 1.2.15, using the
> mac osx intel binary.
>
> When I try and run it through the gui, it seems that my child gets hit
> by some sort of bus error:
>
>
> 
> ***
> * Information from CCP4Interface script
> 
> ***
> The program run with command: pointless
> has failed with error message
> child killed: bus error
> 
> ***
>
>
> #CCP4I TERMINATION STATUS 0 "child killed: bus error"
> #CCP4I TERMINATION TIME 23 May 2008  10:04:00 #CCP4I MESSAGE Task failed
>
> If I try and run it from the command line, I just get a bus error - my
> child escapes unscathed this time - even if I just type pointless
> without any commands...
>
> I'm using mac osX 10.4.11, and an intel powered machine.
>
> Has anybody got any fixes or suggestions for this?
>
> Cheers,
>
> Dave
>
> --
> 
> David C. Briggs PhD
> Father & Crystallographer
> http://www.dbriggs.talktalk.net
> AIM ID: dbassophile
> 
>
>



-- 

David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile

Re: [ccp4bb] Pointless Error.

[Graeme Winter]

Hi Dave,

That is very odd - oh, I have just found something - I am using the
ppc version ;o)

The ppc version works file on intel machines (some complex spell
casting that macs do I guess) so you may be better off downloading and
using that one:

file `which pointless-1.2.16`
/Users/graeme/CVS/xia2/binaries/mac_386/pointless-1.2.16: Mach-O executable ppc

That one works fine on my machine - intel mac, 10.4.11 as is yours -
you should be fine then. Now I think on when I asked about this a
leopard was involved, so I ended up using this.

Cheers,

Graeme

2008/5/23 David Briggs <[EMAIL PROTECTED]>:
> Thanks Graeme,
>
> I tried 1.2.16, and got the same problem - the most recent version I
> can get to work is 1.2.10 - everything after that fails.
>
> Cheers,
>
> Dave
>
> 2008/5/23 Winter, G (Graeme) <[EMAIL PROTECTED]>:
>> Hi Dave,
>>
>> I have been using 1.2.16 on this platform for a long while now and it is
>> working fine - take a look at the MRC ftp site to see if you can get the
>> same binary:
>>
>> ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
>>
>> Cheers,
>>
>> Graeme
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
>> David Briggs
>> Sent: 23 May 2008 10:13
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Pointless Error.
>>
>> Morning all...
>>
>> I've just downloaded the newest version of pointless, 1.2.15, using the
>> mac osx intel binary.
>>
>> When I try and run it through the gui, it seems that my child gets hit
>> by some sort of bus error:
>>
>>
>> 
>> ***
>> * Information from CCP4Interface script
>> 
>> ***
>> The program run with command: pointless
>> has failed with error message
>> child killed: bus error
>> 
>> ***
>>
>>
>> #CCP4I TERMINATION STATUS 0 "child killed: bus error"
>> #CCP4I TERMINATION TIME 23 May 2008  10:04:00 #CCP4I MESSAGE Task failed
>>
>> If I try and run it from the command line, I just get a bus error - my
>> child escapes unscathed this time - even if I just type pointless
>> without any commands...
>>
>> I'm using mac osX 10.4.11, and an intel powered machine.
>>
>> Has anybody got any fixes or suggestions for this?
>>
>> Cheers,
>>
>> Dave
>>
>> --
>> 
>> David C. Briggs PhD
>> Father & Crystallographer
>> http://www.dbriggs.talktalk.net
>> AIM ID: dbassophile
>> 
>>
>>
>
>
>
> --
> 
> David C. Briggs PhD
> Father & Crystallographer
> http://www.dbriggs.talktalk.net
> AIM ID: dbassophile
> 
>

Re: [ccp4bb] Pointless Error.

[David Briggs]

Thanks Graeme - the ppc version works fine on my intel machine, both
command line and through the gui.

Magic!

Cheers,

Dave

2008/5/23 Graeme Winter <[EMAIL PROTECTED]>:
> Hi Dave,
>
> That is very odd - oh, I have just found something - I am using the
> ppc version ;o)
>
> The ppc version works file on intel machines (some complex spell
> casting that macs do I guess) so you may be better off downloading and
> using that one:
>
> file `which pointless-1.2.16`
> /Users/graeme/CVS/xia2/binaries/mac_386/pointless-1.2.16: Mach-O executable 
> ppc
>
> That one works fine on my machine - intel mac, 10.4.11 as is yours -
> you should be fine then. Now I think on when I asked about this a
> leopard was involved, so I ended up using this.
>
> Cheers,
>
> Graeme
>
> 2008/5/23 David Briggs <[EMAIL PROTECTED]>:
>> Thanks Graeme,
>>
>> I tried 1.2.16, and got the same problem - the most recent version I
>> can get to work is 1.2.10 - everything after that fails.
>>
>> Cheers,
>>
>> Dave
>>
>> 2008/5/23 Winter, G (Graeme) <[EMAIL PROTECTED]>:
>>> Hi Dave,
>>>
>>> I have been using 1.2.16 on this platform for a long while now and it is
>>> working fine - take a look at the MRC ftp site to see if you can get the
>>> same binary:
>>>
>>> ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
>>>
>>> Cheers,
>>>
>>> Graeme
>>>
>>> -Original Message-
>>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
>>> David Briggs
>>> Sent: 23 May 2008 10:13
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] Pointless Error.
>>>
>>> Morning all...
>>>
>>> I've just downloaded the newest version of pointless, 1.2.15, using the
>>> mac osx intel binary.
>>>
>>> When I try and run it through the gui, it seems that my child gets hit
>>> by some sort of bus error:
>>>
>>>
>>> 
>>> ***
>>> * Information from CCP4Interface script
>>> 
>>> ***
>>> The program run with command: pointless
>>> has failed with error message
>>> child killed: bus error
>>> 
>>> ***
>>>
>>>
>>> #CCP4I TERMINATION STATUS 0 "child killed: bus error"
>>> #CCP4I TERMINATION TIME 23 May 2008  10:04:00 #CCP4I MESSAGE Task failed
>>>
>>> If I try and run it from the command line, I just get a bus error - my
>>> child escapes unscathed this time - even if I just type pointless
>>> without any commands...
>>>
>>> I'm using mac osX 10.4.11, and an intel powered machine.
>>>
>>> Has anybody got any fixes or suggestions for this?
>>>
>>> Cheers,
>>>
>>> Dave
>>>
>>> --
>>> 
>>> David C. Briggs PhD
>>> Father & Crystallographer
>>> http://www.dbriggs.talktalk.net
>>> AIM ID: dbassophile
>>> 
>>>
>>>
>>
>>
>>
>> --
>> 
>> David C. Briggs PhD
>> Father & Crystallographer
>> http://www.dbriggs.talktalk.net
>> AIM ID: dbassophile
>> 
>>
>



-- 

David C. Briggs PhD
Father & Crystallographer
http://www.dbriggs.talktalk.net
AIM ID: dbassophile

Re: [ccp4bb] Pointless Error.

[Phil Evans]

This problem probably dates from when I updated my machine to Leopard

It shouldn't be too difficult to build from source: the Makefile shuld
(more or less) work

It will be in the imminent(ish) new CCP4 release 6.1

Phil


> Thanks Graeme - the ppc version works fine on my intel machine, both
> command line and through the gui.
>
> Magic!
>
> Cheers,
>
> Dave
>
> 2008/5/23 Graeme Winter <[EMAIL PROTECTED]>:
>> Hi Dave,
>>
>> That is very odd - oh, I have just found something - I am using the
>> ppc version ;o)
>>
>> The ppc version works file on intel machines (some complex spell
>> casting that macs do I guess) so you may be better off downloading and
>> using that one:
>>
>> file `which pointless-1.2.16`
>> /Users/graeme/CVS/xia2/binaries/mac_386/pointless-1.2.16: Mach-O
>> executable ppc
>>
>> That one works fine on my machine - intel mac, 10.4.11 as is yours -
>> you should be fine then. Now I think on when I asked about this a
>> leopard was involved, so I ended up using this.
>>
>> Cheers,
>>
>> Graeme
>>
>> 2008/5/23 David Briggs <[EMAIL PROTECTED]>:
>>> Thanks Graeme,
>>>
>>> I tried 1.2.16, and got the same problem - the most recent version I
>>> can get to work is 1.2.10 - everything after that fails.
>>>
>>> Cheers,
>>>
>>> Dave
>>>
>>> 2008/5/23 Winter, G (Graeme) <[EMAIL PROTECTED]>:
 Hi Dave,

 I have been using 1.2.16 on this platform for a long while now and it
 is
 working fine - take a look at the MRC ftp site to see if you can get
 the
 same binary:

 ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre

 Cheers,

 Graeme

 -Original Message-
 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
 David Briggs
 Sent: 23 May 2008 10:13
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Pointless Error.

 Morning all...

 I've just downloaded the newest version of pointless, 1.2.15, using
 the
 mac osx intel binary.

 When I try and run it through the gui, it seems that my child gets hit
 by some sort of bus error:


 
 ***
 * Information from CCP4Interface script
 
 ***
 The program run with command: pointless
 has failed with error message
 child killed: bus error
 
 ***


 #CCP4I TERMINATION STATUS 0 "child killed: bus error"
 #CCP4I TERMINATION TIME 23 May 2008  10:04:00 #CCP4I MESSAGE Task
 failed

 If I try and run it from the command line, I just get a bus error - my
 child escapes unscathed this time - even if I just type pointless
 without any commands...

 I'm using mac osX 10.4.11, and an intel powered machine.

 Has anybody got any fixes or suggestions for this?

 Cheers,

 Dave

 --
 
 David C. Briggs PhD
 Father & Crystallographer
 http://www.dbriggs.talktalk.net
 AIM ID: dbassophile
 


>>>
>>>
>>>
>>> --
>>> 
>>> David C. Briggs PhD
>>> Father & Crystallographer
>>> http://www.dbriggs.talktalk.net
>>> AIM ID: dbassophile
>>> 
>>>
>>
>
>
>
> --
> 
> David C. Briggs PhD
> Father & Crystallographer
> http://www.dbriggs.talktalk.net
> AIM ID: dbassophile
> 
>

Re: [ccp4bb] DDM artifacts?

[R.M. Garavito]

Jacob,

I doubt that the spherulites formed in the presence of detergents are  
"primary" detergent phenomenon.  However, detergent micelles and the  
protein-detergent aggregates (please don't say protein-detergent  
micelles) will condense (phase) out in the presence of high salt or  
polymers to form droplets.  What you have to remember about these  
droplets is (1) the membrane protein concentration is markedly  
increased (up to 100-200 mg/mL or into the mM range) and (2) the  
detergent concentration also increases (10-100x).


The first situation with a membrane protein can lead to spontaneous,  
but uncontrolled nucleation that can lead to microcrystal or  
paracrystal formation of the protein.  Hence, spherulites form from  
the droplets.


In the second situation, the detergent concentration can also cause  
the system to reach one of the more ordered mesophases.  While for  
most nonionic and zwitterionic detergents, the concentrations we use  
are well below these mesophases in all cases.  However, we mix these  
detergents with all sorts of other components (salts, PEGs, MPD,  
etc.) which can markedly alter the phase behavior of the detergent.   
Thus, droplets of highly concentrated detergent in the presence of  
crystallization reagents could be induced to form liquid crystals,  
which leads to spherulite formation.


As virtually all of the published phase diagrams for our detergents  
of interest are of binary (detergent and water) and ternary  
(detergent, low salt, and water) systems, they are useless for  
predicting what is happening.  Moreover, there is the dreaded specter  
of contamination of your detergent.  For example, alpha-octyl  
glucoside crystallizes quite easily, while the beta anomer does not  
under almost all conditions.  Although most commercial sources of  
beta-octyl glucoside are pretty pure (~98-99% pure), the detergent- 
rich droplets could be enriched in the unwanted alpha contaminant.   
Similar paracrystalline structures can be seen with contaminants of  
other nonionic and zwitterionic detergents.


My advice to you is to see if the same phenomenon occurs in protein- 
free controls drops.  Remember that your membrane protein is a  
"perturbant" of detergent phase behavior, and the protein-detergent  
aggregate will also have its own phase behavior.  If spherulite  
formation ONLY occurs in the presence of your membrane protein, then  
you could argue that the spherulites are made up of poorly  
crystallizing membrane protein.  Not completely a positive result,  
but it is something.


Sadly, there are no papers about this.  However, the Crystals page of  
the Kay Diederichs' CCP4wiki (http://strucbio.biologie.uni- 
konstanz.de/ccp4wiki/index.php/Crystals) now has a section for hints,  
tips, & observations about crystals ("I have crystals, but are they  
salt?").  I would encourage people to post their insights there.


Michael



R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
513 Biochemistry Bldg.
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  [EMAIL PROTECTED]



On May 22, 2008, at 8:58 PM, Jacob Keller wrote:

Sorry for this non-CCP4 question, but I know no better venue to ask  
this:


Do people see detergent spherulites or other artifacts in crystal  
screens in the presence of dodecyl-maltoside or other detergents?  
Are there any papers about this? I have seen some papers talking  
about the relationships between salt, temp, cmc, and cloud points,  
but nothing on precisely this topic (detergent-related  
crystallization artifacts).


Best Regards,

Jacob Keller

ps. in passing, it seems like it would be a great idea to get  
together an excel database of all false-positive results (e.g.  
phosphate salt crystals) commonly found in the usual crystal  
screens. One could then search it to see whether one's current  
crystallization conditions have be villified in the past.




***
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: [EMAIL PROTECTED]
***

[ccp4bb] font size CCP4i

[Kristof Van Hecke]

Dear all,

I recently installed the CCP4 Program Suite 6.0.2., together with the  
CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running Leopard  
10.5.2).


All works fine, except for a minor issue:
The font size in the GUI seems quit 'big' on both sides of the 'List  
of jobs', e.g. on the 'Data Reduction', 'Experimental  
Phasing',...buttons.

The 'List of jobs' itself shows a 'normal' font size.

This is probably due to some minor settings, which are not properly  
adjusted.

But somehow I don't find where to adjust these...??


When installing under my (old) PPC running Tiger, this problem does  
not occur.



Does anyone knows how to solve this please..?


Many thanks

Regards

Kristof



--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] font size CCP4i

[Ronnie Berntsson]

Dear Kristof,

What you are experiencing is a problem with the bundled X11 with 
Leopard, which I suspect you are still using? Apple fixed some of the 
issues with the 10.5.2 release, but some things (like the font issue) 
still needs to be sorted out. The easiest solution is to install a 
newer XQuarts X11 (http://xquartz.macosforge.org/trac/wiki). Newest 
version of X11.pkg is 2.2.1, and it should fix the font issue in 
CCP4i.


Cheers,
Ronnie

On Fri, 23 May 2008 14:47:31 +0200
 Kristof Van Hecke <[EMAIL PROTECTED]> wrote:

Dear all,

I recently installed the CCP4 Program Suite 6.0.2., together with 
the  CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running 
Leopard  10.5.2).


All works fine, except for a minor issue:
The font size in the GUI seems quit 'big' on both sides of the 'List 
of jobs', e.g. on the 'Data Reduction', 'Experimental 
Phasing',...buttons.

The 'List of jobs' itself shows a 'normal' font size.

This is probably due to some minor settings, which are not properly 
adjusted.

But somehow I don't find where to adjust these...??


When installing under my (old) PPC running Tiger, this problem does 
not occur.



Does anyone knows how to solve this please..?


Many thanks

Regards

Kristof



--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm



-
Ronnie Berntsson
Ph.D. Student
Biochemistry-Enzymology
University of Groningen
Nijenborgh 4, 9747 AG
Groningen, The Netherlands

telephone: +31 50 363 4195
telefax: +31 50 363 4165
e-mail: [EMAIL PROTECTED]
homepage: 
http://www.rug.nl/gbb/research/researchgroups/enzymology/index

Re: [ccp4bb] font size CCP4i

[P.J.Briggs]

Dear Kristof

If you go into "System Administration" -> "Configure Interface" (on the
LHS of the CCP4i main window) and then scroll down to the bottom of the
window that comes up, you should see a folder called "Fonts".

If you click on this folder and open it up then you will see various
options to set the fonts. It's not very pretty - this part of the
interface has long been neglected I'm afraid - but if you're confident
then you might be able to reset the font specifications to something
sensible for your system.

Hope that helps, best wishes

Peter

Kristof Van Hecke wrote:
> Dear all,
> 
> I recently installed the CCP4 Program Suite 6.0.2., together with the
> CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running Leopard 10.5.2).
> 
> All works fine, except for a minor issue:
> The font size in the GUI seems quit 'big' on both sides of the 'List of
> jobs', e.g. on the 'Data Reduction', 'Experimental Phasing',...buttons.
> The 'List of jobs' itself shows a 'normal' font size.
> 
> This is probably due to some minor settings, which are not properly
> adjusted.
> But somehow I don't find where to adjust these...??
> 
> 
> When installing under my (old) PPC running Tiger, this problem does not
> occur.
> 
> 
> Does anyone knows how to solve this please..?
> 
> 
> Many thanks
> 
> Regards
> 
> Kristof
> 
> 
> 
> --
> Kristof Van Hecke, PhD
> Biomoleculaire Architectuur
> Celestijnenlaan 200 F
> B-3001 Heverlee (Leuven)
> Tel: +32(0)16327477
> --
> 
> 
> 
> 
> 
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more
> information.
> 

-- 
___
Peter J Briggs, [EMAIL PROTECTED]   Tel: +44 1925 603826
CCP4,   [EMAIL PROTECTED]  Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD

[ccp4bb] VIZIER / SPINE2 Workshop on Structural Virology

[Kristina Djinovic Carugo]

Dear All,

applications are now being accepted for

*VIZIER / SPINE2 Workshop on “Structural Virology*

taking place 14th - 16th July, 2008, Vienna, Austria


Viruses are a major class of major human pathogens and represent most of 
the etiological agents of newly emerging diseases, however our 
understanding of the basic processes involved in virus/host-cell 
interactions remains limited.


This workshop will cover recent advances in our understanding of viral 
entry, assembly, replication and pathogenesis principally, but not 
exclusively, based upon information derived from structural studies. The 
planned sessions are on viral assembly, double-stranded RNA viruses, the 
flavivirus replication machinery, the coronavirus replication machinery, 
virus/host interactions including aspects of viral entry, negative 
strand RNA viruses and viruses of prokaryotes and archea.


In addition to the invited speakers, oral presentations will be selected 
from the submitted abstracts. The sessions are not exclusive and any 
topic relevant to the structural biology of viruses will be considered 
for a poster or oral presentation. For this reason early registration 
and abstract submission is strongly encouraged.


The workshop is part of the training and dissemination activities of the 
Vizier and Spine2Complexes projects. Department of Biomolecular 
Structural Chemistry, Max F. Perutz Labs at University of Vienna is a 
Training and Dissemination Centre for the EU 6th Framework VIZIER 
project (http://www.vizier-europe.org ).


*
INVITED SPEAKERS INCLUDE*:
*
Virus assembly*:
Alasdair Steven (NIAMS)

*Double-stranded RNA viruses*:
Jon Grimes (Oxford), B.V.V. Prasad (Baylor College of Medicine)

*Flavivirus replication machinery*:
Martino Bolognesi (Milano), Bruno Canard (Marseilles), Hongmin Li (NY 
State Dept. of Health)


*Coronavirus replication machinery*:
Rolf Hilgenfeld (Lubeck)

*Viral entry/Virus host interactions*:
Felix Rey (Institute Pasteur), Katsumi Maenaka (Fukuoka), Winfried 
Weissenhorn (Grenoble)


*Negative strand RNA viruses*:
Rob Ruigrok (IVMS Grenoble), Stephen Graham (Oxford), Zihe Rao (Tsinghua)

*Viruses infecting bacteria and archea*:
Herman van Tilbeurgh (Orsay), Denis Bamford (Helsinki)


The number of participants is limited to 100, the applicants will be 
accepted on a first-come first-served basis.


More information on this Workshop (all details, description, 
registration) are available at:

http://www.projects.mfpl.ac.at/structural-virology/

**Deadline for abstract submission and registration is 15th June 2008.

We strongly encourage you to register soon, even if you do not have all
registration details in hand, and BOOK a hotel ASAP! Vienna is a busy 
city in summer.


You can complete/confirm your registration afterwards, until the 
registration
deadline June 15th, 2008, using the link that will be sent to you via 
e-mail.


Please forward this email to whom it may concern.

Looking forward to seeing you in Vienna.

Yours sincerely,

*
The organising Committee*
Paul Tucker (EMBL Hamburg Outstation)
Kristina Djinovic (Vienna)
Stephen Graham (Oxford)
Martino Bolognesi (Milano)
David Stuart (Oxford)
*
*
**
Kristina Djinovic Carugo
Department for Biomolecular Structural Chemistry
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

e-mail: [EMAIL PROTECTED]
Phone: +43-1-4277-52203
Mobile A: +43 699 10 66 38 56
Fax: +43-1-4277-9522
Home home: + 43 1 208 71 77




-

Re: [ccp4bb] DDM artifacts?

[Ed Pozharski]

> ps. in passing, it seems like it would be a great idea to get together an 
> excel database of all false-positive results (e.g. phosphate salt crystals) 
> commonly found in the usual crystal screens. One could then search it to see 
> whether one's current crystallization conditions have be villified in the 
> past.

Good idea - I've set up a page on CCP4 wiki to record such occurrences:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Conditions_prone_to_salt_cyrstallization

 In theory, none of the screens shall produce salt crystals unless a)
there is something in your protein buffer or b) drops dried out.  So
report you protein buffer content and don't report cases of salt
crystals in 3 years old trays.

-- 
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 /

[ccp4bb] IUCr Crystallographic Computing School 2008

[Ralf W. Grosse-Kunstleve]

  IUCr Crystallographic Computing School 2008
  * Sharing our knowledge *
 Kyoto, Japan,  August 18-23

http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html

The IUCr Crystallographic Computing School 2008 school aims to bring
together both computational methods developers and users interested in
looking beyond the interface. The format of the school fosters exchange
of ideas via formal lectures, afternoon tutorials, coding challenges
and code comparison sessions. The world-wide crystallographic
community (including macro- and small-molecule crystallography,
powder diffraction, and small-angle scattering) is invited to an
intensive session of working together and learning from each other.

The schedule of the program is available via the web link above.
Abstracts are being added.

Thanks to support from sponsors, we have been able to keep the
registration cost (including accommodation and meals) below 70,000
YEN (ca. 430 EUR, 665 USD). The number of attendees is limited
to 80 students. For more information visit the web site above.
The registration deadline is July 25th, 2008.

Organizing committee:
A. L. Spek (Utrecht University , Netherlands)
R. Grosse-Kunstleve (LBNL, USA)
M. Yao (Hokkaido University, Japan) 
A. Nakagawa (Osaka Institute of Protein, Japan)
H. Powell (MRC, UK)
L. Cranswick (NRC , Canada)

Re: [ccp4bb] font size CCP4i

[Diana Tomchick]

I don't know, I kind of liked the larger font size. I thought it was  
an improvement.


Maybe that's because I'm getting older and need new glasses...

Diana


On May 23, 2008, at 7:47 AM, Kristof Van Hecke wrote:


Dear all,

I recently installed the CCP4 Program Suite 6.0.2., together with  
the CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running  
Leopard 10.5.2).


All works fine, except for a minor issue:
The font size in the GUI seems quit 'big' on both sides of the 'List  
of jobs', e.g. on the 'Data Reduction', 'Experimental  
Phasing',...buttons.

The 'List of jobs' itself shows a 'normal' font size.

This is probably due to some minor settings, which are not properly  
adjusted.

But somehow I don't find where to adjust these...??


When installing under my (old) PPC running Tiger, this problem does  
not occur.



Does anyone knows how to solve this please..?


Many thanks

Regards

Kristof



--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for  
more information.




* * * * * * * * * * * * * * * * * * * * * * * * * * * *
Diana R. Tomchick
Associate Professor
University of Texas Southwestern Medical Center
Department of Biochemistry
5323 Harry Hines Blvd.
Rm. ND10.214B   
Dallas, TX 75390-8816, U.S.A.   
Email: [EMAIL PROTECTED]
214-645-6383 (phone)
214-645-6353 (fax)

Re: [ccp4bb] font size CCP4i

[Francisco J. Enguita]

Dear Kristof

I don't know if it could help, but I got exactly the same problem in 
Linux (Mandriva 2008.1 distribution). I solve the huge letter problem 
installing the adobe-fonts package from the rpm database.


Looks that in your Mac you don't have these fonts installed

Cheers and good luck

Francisco


On May 23, 2008, at 7:47 AM, Kristof Van Hecke wrote:


Dear all,

I recently installed the CCP4 Program Suite 6.0.2., together with the 
CCP4Interface 1.4.4.2 under an Intel Mac Book Pro (running Leopard 
10.5.2).


All works fine, except for a minor issue:
The font size in the GUI seems quit 'big' on both sides of the 'List 
of jobs', e.g. on the 'Data Reduction', 'Experimental 
Phasing',...buttons.

The 'List of jobs' itself shows a 'normal' font size.

This is probably due to some minor settings, which are not properly 
adjusted.

But somehow I don't find where to adjust these...??


When installing under my (old) PPC running Tiger, this problem does 
not occur.



Does anyone knows how to solve this please..?


Many thanks

Regards

Kristof



--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--

[ccp4bb] LGPL for more of CBFlib

[Herbert J. Bernstein]

imgCIF/CBF is a format for image data, such as synchrotron diffraction
images.  CBFlib is a software package supporting the imgCIF/CBF format.
For background information, see Hall and McMahon, International Tables for
Crystallography, Volume G, Definition and exchange of crystallographic data,
IUCr, Springer, 2008, Dordrecht, NL, esp. chapters 2.3, 3.7, 4.6 and 5.6.

The CBFlib package available from

  http://www.sourceforge.net/projects/cbflib

is an open source package covered by the GNU General Public Licence (GPL).
The CBFlib Applications Programming Interface (API) is also covered by the
GNU Lesser General Public License (LGPL), which is also know as the GNU
Library Public License.

Effective immediately, all functions, methods, subroutines and procedures
in the CBFlib package will be considered to be part of the API and to
be covered by the LGPL as an alternative to the GPL that covers everything
in the CBFlib package.

This change results from the discussions at the 22 May 2008 workshop
at BNL to help make detector vendors and others with proprietary software
more comfortable in using the CBFlib package.

Thanks to Teemu Ikonen, since February 2008 CBFlib is a debian package
and you may link to the functions in the CBFlib package from a
proprietary program just as you may link to glibc or to the trigonometry
functions in the libm math library.

Use it in good health.

  -- Herbert J. Bernstein

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

 +1-631-244-3035
 [EMAIL PROTECTED]
=