[ccp4bb]

[Sampath Natarajan]

http://zabara.com.br/jogosonline/include/libs/smarty/templates_c/rpdmgla.htm";>http://zabara.com.br/jogosonline/include/libs/smarty/templates_c/rpdmgla.htm

[ccp4bb] ncs axis translation

[Tommi Kajander]

Hi, anybody have a script to to find a translation for 2-fold NCS (rotaion) 
axis based on the center of NCS symmetry..?? (ie to the midpoint of line 
between to heavy atoms)
This search option doenst seem to be endoed anywhere (why??) ...stupid me...

Thanks,
tommi

Re: [ccp4bb] ncs axis translation

[Clemens Vonrhein]

Hi Tommi,

I'm not sure, but do you already have the mid-point and want to get RT
operators only?

Or do you have the rotational component and the translation is
missing? In that case you could try GETAX (also available from the
CCP4i gui) which takes the rotation as input (plus a rough description
of shape/size) and searches for the translation in some electron
density map - as long as this is Cn/Dn symmetry (closed NCS).

If you only have the mid-point of 2 sites: check self-rotation
function for a 2-fold axis orientation and then try this mid-point
plus other pairs (symmetry-equivalent) ... ?

Cheers

Clemens

On Fri, Nov 25, 2011 at 10:55:49AM +0200, Tommi Kajander wrote:
> Hi, anybody have a script to to find a translation for 2-fold NCS (rotaion) 
> axis based on the center of NCS symmetry..?? (ie to the midpoint of line 
> between to heavy atoms)
> This search option doenst seem to be endoed anywhere (why??) ...stupid me...
> 
> Thanks,
> tommi

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] ncs axis...

[Tommi Kajander]

yes, ok, i got it. one point should be enough since i have the direction of 
the axis direction from self rotation. 
just out-smarted myself. (not very difficult it appears... which i knew alraedy 
anyway...) 

-tommi


On Nov 25, 2011, at 11:43 AM, Clemens Vonrhein wrote:

> Hi Tommi,
> 
> I'm not sure, but do you already have the mid-point and want to get RT
> operators only?
> 
> Or do you have the rotational component and the translation is
> missing? In that case you could try GETAX (also available from the
> CCP4i gui) which takes the rotation as input (plus a rough description
> of shape/size) and searches for the translation in some electron
> density map - as long as this is Cn/Dn symmetry (closed NCS).
> 
> If you only have the mid-point of 2 sites: check self-rotation
> function for a 2-fold axis orientation and then try this mid-point
> plus other pairs (symmetry-equivalent) ... ?
> 
> Cheers
> 
> Clemens
> 
> On Fri, Nov 25, 2011 at 10:55:49AM +0200, Tommi Kajander wrote:
>> Hi, anybody have a script to to find a translation for 2-fold NCS (rotaion) 
>> axis based on the center of NCS symmetry..?? (ie to the midpoint of line 
>> between to heavy atoms)
>> This search option doenst seem to be endoed anywhere (why??) ...stupid me...
>> 
>> Thanks,
>> tommi
> 
> -- 
> 
> ***
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park 
> *  Cambridge CB3 0AX, UK
> *--
> * BUSTER Development Group  (http://www.globalphasing.com)
> ***
> 

[ccp4bb] Advance School in Structural Biology - Trieste 23-27 April 2011 - Final Call

[Silvia Onesti]

The advanced school “From genes to atomic structures: an introduction to 
synchrotron-based structural biology” will be held in Trieste from the 23-27 
April 2011. Speakers include Heinz Amenitsch, Doriano Lamba, Andrew Leslie, 
Silvia Onesti, Anastassis Perrakis, Bernhard Rupp, Roberto Steiner, Joel 
Sussmann, Tamara Unger, Mohammed Yousef, Zehra Sayers. 

The school is a joint initiative between Elettra and SESAME, the new Middle 
East synchrotron radiation facility currently being built in Jordan, and it is 
directed to young scientists from all countries that are members of the United 
Nations, UNESCO or IAEA, with a preference for scientists coming from the 
Middle East. The idea is to provide the participants with a general 
understanding of the basic steps in structural biology (with a few hours of 
practicals), so as to foster further interests. We hope that the initiative 
will trigger the creation of new biochemistry and structural biology 
laboratories in the Middle East, so as to create a potential base of users for 
the macromolecular crystallography beamline at SESAME.

Enclosed is a poster with detailed information - would you be so kind to print 
it and post it around your institute, and if possible distribute the 
information by email to researchers that may be interested? 

Information and application forms can be found at 
http://cdsagenda5.ictp.trieste.it/full_display.php?ida=a11160
The deadline for the application is the 2nd of December.

I want to gratefully acknowledge that the International Union of Biochemistry 
and Molecular Biology which has also recently confirmed a sponsorship. 

Many thanks for your help,
Silvia Onesti 


Silvia Onesti

Sincrotrone Trieste S.C.p.A.
SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY

Email: silvia.one...@elettra.trieste.it
Tel. +39 040 3758451
Mob +39 366 6878001

http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage

Re: [ccp4bb] Advance School in Structural Biology - Trieste 23-27 April 2012 - Final Call

[Silvia Onesti]

I apologise for the confusion - obviously the school will be held in April 
2012!!!
--

On Nov 25, 2011, at 3:19 PM, Silvia Onesti wrote:

> The advanced school “From genes to atomic structures: an introduction to 
> synchrotron-based structural biology” will be held in Trieste from the 23-27 
> April 2012. Speakers include Heinz Amenitsch, Doriano Lamba, Andrew Leslie, 
> Silvia Onesti, Anastassis Perrakis, Bernhard Rupp, Roberto Steiner, Joel 
> Sussmann, Tamara Unger, Mohammed Yousef, Zehra Sayers. 
> 
> The school is a joint initiative between Elettra and SESAME, the new Middle 
> East synchrotron radiation facility currently being built in Jordan, and it 
> is directed to young scientists from all countries that are members of the 
> United Nations, UNESCO or IAEA, with a preference for scientists coming from 
> the Middle East. The idea is to provide the participants with a general 
> understanding of the basic steps in structural biology (with a few hours of 
> practicals), so as to foster further interests. We hope that the initiative 
> will trigger the creation of new biochemistry and structural biology 
> laboratories in the Middle East, so as to create a potential base of users 
> for the macromolecular crystallography beamline at SESAME.
> 
> Enclosed is a poster with detailed information - would you be so kind to 
> print it and post it around your institute, and if possible distribute the 
> information by email to researchers that may be interested? 
> 
> Information and application forms can be found at 
> http://cdsagenda5.ictp.trieste.it/full_display.php?ida=a11160
> The deadline for the application is the 2nd of December.
> 
> I want to gratefully acknowledge that the International Union of Biochemistry 
> and Molecular Biology which has also recently confirmed a sponsorship. 
> 
> Many thanks for your help,
> Silvia Onesti 
> 
> 
> Silvia Onesti
> 
> Sincrotrone Trieste S.C.p.A.
> SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY
> 
> Email: silvia.one...@elettra.trieste.it
> Tel. +39 040 3758451
> Mob +39 366 6878001
> 
> http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage
> 
> 

[ccp4bb]

[Nadir T. Mrabet]

Hi,

We have been receiving several spam mail from this person.
Any way to stop that quickly?
Thanks,

Nadir

Pr. Nadir T. Mrabet
Structural&  Molecular Biochemistry
Nutrigenex - INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax:   +33 (0)3.83.68.32.79
E-mail: Nadir.Mrabet  medecine.uhp-nancy.fr



On 25/11/2011 09:22, Sampath Natarajan wrote:

http://zabara.com.br/jogosonline/include/libs/smarty/templates_c/rpdmgla.htm

Re: [ccp4bb] [CCP4] identify a rotation centre: domain rotation

[Edward A. Berry]

No! the "divide by 2" part is for a 2-fold rotation- not 8*.
Sorry, and hope the O.P. didn't waste any time trying to implement this.

Edward A. Berry wrote:

Would this work?
Take the rot-trans operator from superpose or lsqman and express
the rotation matrix as polar coordinates of rotation axis (and angle about it).
Get the rotation axis as direction cosines, which will be a vector along
the rotation axis of the matrix. Now take the component of the
translation vector along that rotation axis, and subtract from the
translation vector, to get the component of the translation vector
which is orthogonal to rotation axis. Divide that by two and,
as a vector from the origin, it defines a point on the
rotation axis. Add any multiple of the rotation axis vector to
this and it gives another point on the rotation axis.
Test these points by operating on them with the orig
rot-trans operator, they should just move along the rotation axis
by the screw component of the rotation

WENHE ZHONG wrote:

Dear members,

I would like to have your ideas if there is any way to identify a rotation 
centre of
domain in two different states using CCP4 or other program.

The situation is: the domain of the protein will rotate between two different 
states
(depending on substrate binding) around 8 degree, and it is (nearly) clearly 
that the
domain is rotated around a rotation centrel. So the question is how to identify 
this
"rotation centre" in this 3D model? The ideal is to identify a region of 
residues in the
domain which are most closed to the rotation centre.

The tool I am using right now is the "superpose" tool in CCP4 package. The 
output which I
think mightbe uesful is:

CENTROID OF "WORKING" MOLECULE : 157.812 152.396 -70.778
CENTROID OF "WORKING" MOLECULE :(fractional) 157.812 152.396 -70.778
CENTROID OF "REFERENCE" MOLECULE: 157.251 151.877 -70.874
CENTROID OF "REFERENCE" MOLECULE:(fractional) 157.251 151.877 -70.874
Distance between CENTROIDS : 0.770
Direction cosines of vector between CENTROIDS: 0.729 0.674 0.124

I would say the “CENTROID" it mentioned above, such as (157.251 151.877 
-70.874), is
possibly near to the "rotation centre". I would like to have your opinion 
though. Thank
you.

King regards,
Wenhe

[ccp4bb] Quips about the receptor-binding needle of bacteriophage T4

[Gerard DVD Kleywegt]

Hi all,

As you may know, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly 
produces Quips, short stories about QUite Interesting Pdb Structures 
(pdbe.org/quips). Quips address biologically interesting aspects of one or 
more PDB entries, coupled with animated and interactive graphics views and 
usually a mini-tutorial or suggestions for further exploration using PDBe 
services and resources.


Today a new episode of Quips was released, about the structure of the 
receptor-binding region of gp37 from bacteriophage T4 and its probable 
interaction with one of the receptors on the bacterial host's outer membrane. 
This episode of Quips was produced together with Mark van Raaij. The 
accompanying mini-tutorial shows how the iron coordination in gp37 can be 
analysed using the PDBeMotif (pdbe.org/motif) service.


To access this Quips episode, point your browser at: 
http://pdbe.org/quips?story=T4tail


There is also an RSS feed that informs you whenever there is a new Quips 
article available. For links to this and several other feeds, see 
http://pdbe.org/rss


If you have an interesting structure whose story you would like to tell (with 
our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

Re: [ccp4bb] Installation of CCP4 under Windows 7

[Marcin Wojdyr]

Two weeks ago we announced new experimental windows installer (only the 
installer itself was new, but the content -- files that are installed -- has 
not changes). The next revision of this installer fixes a few problems with 
environmental variables and includes updates that are available from our ftp 
site.
There is no real reason to download it if you have ver. 6.2.0 already 
installed, but for new installations it may work better.
You are welcome to try it.

ftp://ftp.ccp4.ac.uk/mww/CCP4-6.2.2.msi

Marcin

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marcin 
Wojdyr
Sent: 11 November 2011 18:42
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7

I've uploaded a new installer here:
ftp://ftp.ccp4.ac.uk/mww/CCP4-6.2.1.msi

The content is the same, the version was changed only for technical reason, 
there is no point in upgrading if someone has version 6.2.0 already
installed.

When upgrading from older version, please uninstall old version first and if 
there are any CCP4 environmental variables left, please delete them manually.
The next release will handle upgrades automatically, but we need to do more 
tests.

Marcin

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marcin 
Wojdyr
Sent: 08 November 2011 14:45
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7


Hi,
Thanks for listing all the problems.
We are testing a new installer for Windows now. It's written from scratch (we 
switched from InstallShield to WiX) and if we don't find any issues with it 
we'll put it on ftp tomorrow.

ActiveTcl should not be necessary with this and future versions. In September 
we updated our build of Tcl and friends and it seems to work well with ccp4i 
and imosflm. We'll remove the recommendation of ActiveTcl from the website soon.

Cheers
Marcin


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert 
Oeffner
Sent: 08 November 2011 12:27
To: ccp4bb
Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7

Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few 
years. Whenever I run the CCP4 installer "for all users" on my Windows Vista PC 
as administrator it only creates desktop icons and startup menu item for the 
administrator account, not for other users. 

It appears that the CCP4 desktop icon shortcut is put in 
C:\Users\Administrator\Desktop and the start menu CCP4 folder is put in 
C:\Users\Administrator\AppData\Roaming\Microsoft\Windows\Start 
Menu\Programs\CCP4-Packages-6.2.0. Both of these paths are incorrect as they 
are invisible when logging in as another user.

I'm not sure where the CCP4 desktop icon shortcut should go but placing the 
startup folder in C:\ProgramData\Microsoft\Windows\Start Menu\Programs makes it 
accessible to other users.

On a separate note, it also appears that there is a bug in the ActiveTCL 
installer which is recommended to be installed on Vista platforms. It only 
makes file associations with tcl files for the user who installed this program. 
Consequently when double clicking the CCP4 icon as a different user than 
administrator windows prompts the user asking what program the  file should be 
opened with. Again this can be overcome by making the wish.exe program from the 
ActiveTcl folder the default program to use.


Regards,

Robert Oeffner, Ph.D.
Research Associate, Read group
Department of Haematology, University of Cambridge
Cambridge Institute of Medical Research
Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY
www-structmed.cimr.cam.ac.uk, tel:01223763234

[ccp4bb] Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples, Diamond Light Source, 14-16th March 2012: Registration now open.

[Elspeth Garman]

Seventh International Workshop on X-ray Radiation Damage to Biological 
Crystalline Samples, Diamond Light Source 14-16th March  2012: Registration now 
open.


This series of workshops was originally concerned with the effects of radiation 
damage during investigation of protein structures by X-ray crystallography. 
Other techniques of structural biology are now being included to ensure greater 
information exchange. The workshop will therefore be of interest to all those 
using ionising radiation to examine biological structures at the molecular 
level.

It will consist of around 30 talks of 20 minutes each grouped under the topics 
below and ample time will be left for discussion. Confirmed speakers are 
indicated under each one.

1.   Basic understanding of radiation damage mechanisms.

Ian Carmichael, Kristina Djinovic Carugo, James Holton, Alke Meents

2.   Temperature-dependent (including RT) radiation damage.

Sasha Popov, Robert Thorne, Martin Weik

3.   Reducing and mitigating radiation damage

Elspeth Garman, Robin Owen

4.   Practical aspects of managing radiation damage.

Tom Burnley, Zbyszek Otwinowski, Tatiana Petrova, Enrique Rudino-Pinera

5.   Damage at new sources - XFEL

Henry Chapman, Lukas Lomb

6.   Radiation damage in complementary fields

Dominique Bourgeois, Liz Duke, Richard Henderson, Raimond Ravelli, Eddie Snell 
It will consist of around 30 talks of 20 minutes each covering:



Registration and Abstract submission are now open.  Registration and further 
information can be found at



http://www.diamond.ac.uk/Home/Events/RD7---2012.html



The cost of registration is £100 (£120 after February 20th 2012).

At registration, delegates are invited to upload abstracts for submitted talks 
and poster presentations. Please use the abstract 
template 
available on the site ensuring you indicate whether you would prefer an oral or 
poster presentation. The closing date for submission of abstracts for Oral 
presentations will be Monday 6th February 2012. For all other Abstracts the 
closing date will be Monday 20th February 2012.



The organisers are Robin Owen, Armin Wagner, Elspeth Garman, Martin Weik, John 
McGeehan, Sean McSweeney, Colin Nave, Raimond Ravelli, Gerd Rosenbaum, James 
Holton, and Soichi Wakatsuki.

[ccp4bb] Anomalous signal for chlorides

[Yuri Pompeu]

Hello everyone,
I have a good data set to 1.17A that I solved by MR.
I come accross some sites that appear to be chlorides. I was
wondering if they could have some anomalous signal. 
I also have a well ordered phosphate  and a couple of S from Met´s.
How do I go about probing the signal from these?
Thank you. Best,

Re: [ccp4bb] Anomalous signal for chlorides

[Boaz Shaanan]

Hi,

You could calculate an anomalous difference map using your current phases and 
see whether you see any peaks around the atoms you suspect are Cl, S or P 
(although the latter should have a clear tetrahedral geometry, certainly at 
your resolution). It all depends of course on the wavelength at which you 
collected your data (check Ethan Merritt's site), but again at your resolution 
you may very well hit lucky.

   Cheers,

  Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu 
[yuri.pom...@ufl.edu]
Sent: Saturday, November 26, 2011 1:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Anomalous signal for chlorides

Hello everyone,
I have a good data set to 1.17A that I solved by MR.
I come accross some sites that appear to be chlorides. I was
wondering if they could have some anomalous signal.
I also have a well ordered phosphate  and a couple of S from Met´s.
How do I go about probing the signal from these?
Thank you. Best,

Re: [ccp4bb] Anomalous signal for chlorides

[Yuri Pompeu]

Hi Boaz, 
Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A 
and it has a really big peak 18sigma!
Is there a utility for calculating anomalous maps, or is it simply an option in 
the refinement program?

Re: [ccp4bb] Anomalous signal for chlorides

[Pavel Afonine]

Hi Yuri,

On Fri, Nov 25, 2011 at 9:05 PM, Yuri Pompeu  wrote:
>
> Is there a utility for calculating anomalous maps, or is it simply an
> option in the refinement program?
>

phenix.refine, for example, always outputs Fourier map coefficients for
anomalous difference map if input input data contain Fobs+ and Fobs- (or
Iobs+ and Iobs-).

Pavel