[ccp4bb] Detwin

[Careina Edgooms]

Dear CCP4

I have data that is twinned with an L statistic of 0.43. It seems all the 
crystals that I produced were twinned sadly. Is there anything I can do to 
twinned data to make it easier to analyse?
I have tried to use the detwin software but it won't let me input a 
twinning operator for a standard transformation. I am not sure why? My space 
group is P21.
Thanks for your help
Careina

Re: [ccp4bb] Detwin

[Herman . Schreuder]

Dear Careina,
 
if 0.43 is the twin fraction, you might not be able to detwin your data,
since the twin fraction is very close to 0.5. If you plan to solve your
structure with molecular replacement, I would just run the molecular
replacement with the twinned data and refine the structure with Refmac
using the twin mode. Twinned electron density maps can look much better
than you may expect, since the unmodeled twin molecule does not
contribute to the phases and will "only" generate some noise. If plan to
apply de novo phasing, that will be another story
 
Best regards,
Herman




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Careina Edgooms
Sent: Monday, December 10, 2012 10:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Detwin


Dear CCP4

I have data that is twinned with an L statistic of 0.43. It
seems all the crystals that I produced were twinned sadly. Is there
anything I can do to twinned data to make it easier to analyse?
I have tried to use the detwin software but it won't let me
input a twinning operator for a standard transformation. I am not sure
why? My space group is P21.
Thanks for your help
Careina

[ccp4bb] CCP4 Study Weekend 2013 - last day for registration!

[ronan . keegan]

Dear All,

One final reminder about next month's CCP4 Study Weekend. Registration will 
close today, Monday the 10th of December. The meeting will take place at the 
East Midlands Conference Centre in Nottingham, UK from the 3rd to the 5th of 
January and is entitled "Molecular Replacements", focusing on the presentation 
and discussion of advanced methods and techniques in this important field. For 
more information about the meeting and to register please visit the Study 
Weekend website at:

http://www.cse.scitech.ac.uk/events/CCP4_2013/

We look forward to seeing you in Nottingham.

Best wishes,

Ronan

-- 
Scanned by iCritical.

[ccp4bb] Nobel Prize Quips

[Gary Battle]

 Nobel Prize Quips: Explore the structure of B2AR bound to its G-protein.

Today, Nobel Laureates Robert J. Lefkowitz and Brian K. Kobilka take 
center stage in Stockholm where they will receive their Nobel Prize 
Medals for their studies of G-protein--coupled receptors (GPCRs).


To mark this occasion we have written a special Quips article which 
explores the Nobel Prize winning structure of B2AR bound to its G-protein.


http://pdbe.org/quips?story=B2AR

GPCRs are signalling proteins which enable cells to communicate with 
each other and the surrounding environment. They provide the molecular 
framework and mechanism for the transmission of a wide variety of 
signals over the cell membrane, between cells and over long distances in 
the body. In this Quips you will learn how the structure of B2AR bound 
to its G-protein helped explain how binding of a small molecule on one 
face of B2AR activates the G-protein.


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 


Best Regards,
Gary.

--
Gary Battle
PDBe Outreach Coordinator

http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

Re: [ccp4bb] Detwin

[Sergei Strelkov]

Dear Careina,

Could you please let us know what your cell parameters are?
And what is the twin law ('transformation') that you suspect?

Best wishes,
Sergei



Dear CCP4

I have data that is twinned with an L statistic of 0.43. It seems all 
the crystals that I produced were twinned sadly. Is there anything I 
can do to twinned data to make it easier to analyse?
I have tried to use the detwin software but it won't let me input a 
twinning operator for a standard transformation. I am not sure why? My 
space group is P21.

Thanks for your help
Careina

[ccp4bb] Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.

[Robert Sweet]

We are offering RapiData 2013, the fifteenth offering of our popular 
course:


Rapid Data Collection and Structure Solving at the NSLS: A Practical
   Course in Macromolecular X-Ray Diffraction Measurement

The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. 
Students could be at any level from advanced undergraduate to full professor. 
The course should accommodate 48 students total.  We encourage all students to 
bring their own specimens for data collection, and to bring old data for the 
data-reduction and structure-solving tutorials.


Please read the Course Announcement at http://www.bnl.gov/RapiData/.
You'll see that many experts in the field will be available for lectures
and tutorials. You'll find the application materials on the Course
Application tab at this site.

For the eleventh time we will hold a short lecture course on the 
fundamentals of crystallography for roughly five hours on Sunday 21 April. 
The body of the RapiData course really requires that students have a 
healthy knowledge of crystallography.  For potential students who have 
some experience but are shaky about fundamentals, this course will help. 
There will be a small additional fee for the fundamentals course, to pay 
for Saturday night accomodations and food on Sunday morning and noon.


Latin American Scientists: Several scholarships are available, from the
International Union of Crystallography, to pay partial travel and
subsistence costs for Latin-American students and junior faculty (under 40 
yrs).  Please apply for the course, and then contact R. Sweet

(sw...@bnl.gov) if you are interested in applying for a scholarship.

In accordance with the standards of the International Union of
Crystallography, we observe the basic policy of non-discrimination,
affirming the right and freedom of scientists to associate in
international scientific activity without regard to such factors as
citizenship, religion, creed, political stance, ethnic origin, race,
colour, language, age, or gender, in accordance with the Statutes of the
International Council for Science.  At this course no barriers will exist
beyond the application procedure that would prevent the participation of
bona fide scientists.

Please apply or send your students to our course,

Bob Sweet, Sonya Kiss, and Alex Soares

Course Announcement at http://www.bnl.gov/RapiData/

=
Robert M. Sweet E-Dress: sw...@bnl.gov
Group Leader, PXRR: Macromolecular   ^ (that's L
  Crystallography Research Resource at NSLSnot 1)
  http://px.nsls.bnl.gov/
Photon Sciences and Biology Dept
Mail Stop, Bldg 463
Brookhaven Nat'l Lab.   Phones:
Upton, NY  11973631 344 3401  (Office)
U.S.A.  631 344 2741  (Facsimile)
=

[ccp4bb] CCP4 Study Weekend 2013 - Diamond MX User Meeting programme

[ralf . flaig]

Dear colleagues,

further to Ronan's email I would like to let you know that the programme for 
the Diamond MX User Meeting taking place Thursday 3 January 2013 is now 
available at:

http://www.cse.scitech.ac.uk/events/CCP4_2013/user_group.html

We look forward to seeing you there.

Best regards,
Ralf



--
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] Coot keybinding for fixing an atom in place

[Sam Stampfer]

Dear CCP4 Bulletin Board,

Does anyone have a keybinding I can add to my .coot file so that I can hit
a key (for example, Shift-F) to fix in place the actively selected atom,
without having to go through the fixed atoms dialog box? Also, does anyone
have a keybinding for "Clear Fixed Atoms"?

Thanks!

-Sam

Re: [ccp4bb] Coot keybinding for fixing an atom in place

[Debreczeni, Judit]

off the top of my head (i.e. not tested):



(add-key-binding "fix atom" "F"

(lambda () (mark-atom-as-fixed (car (active-residue)) (cdr
(active-residue)) 1)))



(add-key-binding "clear fixed atoms" "D"

   (lambda () (clear-fixed-atoms-all)))









From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sam Stampfer
Sent: 10 December 2012 16:22
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coot keybinding for fixing an atom in place



Dear CCP4 Bulletin Board,

Does anyone have a keybinding I can add to my .coot file so that I can
hit a key (for example, Shift-F) to fix in place the actively selected
atom, without having to go through the fixed atoms dialog box? Also,
does anyone have a keybinding for "Clear Fixed Atoms"?

Thanks!

-Sam


--
AstraZeneca UK Limited is a company incorporated in England and Wales with 
registered number: 03674842 and a registered office at 2 Kingdom Street, 
London, W2 6BD.
Confidentiality Notice: This message is private and may contain confidential, 
proprietary and legally privileged information. If you have received this 
message in error, please notify us and remove it from your system and note that 
you must not copy, distribute or take any action in reliance on it. Any 
unauthorised use or disclosure of the contents of this message is not permitted 
and may be unlawful.
Disclaimer: Email messages may be subject to delays, interception, non-delivery 
and unauthorised alterations. Therefore, information expressed in this message 
is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by 
an authorised representative independent of this message. No contractual 
relationship is created by this message by any person unless specifically 
indicated by agreement in writing other than email.
Monitoring: AstraZeneca UK Limited may monitor email traffic data and content 
for the purposes of the prevention and detection of crime, ensuring the 
security of our computer systems and checking Compliance with our Code of 
Conduct and Policies.

Re: [ccp4bb] Coot keybinding for fixing an atom in place

[Sam Stampfer]

Thanks for your help! That is close, but it will only fix the alpha carbon
of the selected residues.

On Mon, Dec 10, 2012 at 1:11 PM, Debreczeni, Judit <
judit.debrecz...@astrazeneca.com> wrote:

>  off the top of my head (i.e. not tested):
>
> ** **
>
> (add-key-binding "fix atom" "F"
>
> (lambda () (mark-atom-as-fixed (car (active-residue)) (cdr
> (active-residue)) 1)))
>
> ** **
>
> (add-key-binding "clear fixed atoms" "D"
>
>(lambda () (clear-fixed-atoms-all)))
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
>  --
>
> AstraZeneca UK Limited is a company incorporated in England and Wales with
> registered number: 03674842 and a registered office at 2 Kingdom Street,
> London, W2 6BD.
>
> *Confidentiality Notice: *This message is private and may contain
> confidential, proprietary and legally privileged information. If you have
> received this message in error, please notify us and remove it from your
> system and note that you must not copy, distribute or take any action in
> reliance on it. Any unauthorised use or disclosure of the contents of this
> message is not permitted and may be unlawful.
>
> *Disclaimer:* Email messages may be subject to delays, interception,
> non-delivery and unauthorised alterations. Therefore, information expressed
> in this message is not given or endorsed by AstraZeneca UK Limited unless
> otherwise notified by an authorised representative independent of this
> message. No contractual relationship is created by this message by any
> person unless specifically indicated by agreement in writing other than
> email.
>
> *Monitoring: *AstraZeneca UK Limited may monitor email traffic data and
> content for the purposes of the prevention and detection of crime, ensuring
> the security of our computer systems and checking compliance with our Code
> of Conduct and policies.
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Sam
> Stampfer
> *Sent:* 10 December 2012 16:22
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Coot keybinding for fixing an atom in place
>
> ** **
>
> Dear CCP4 Bulletin Board,
>
> Does anyone have a keybinding I can add to my .coot file so that I can hit
> a key (for example, Shift-F) to fix in place the actively selected atom,
> without having to go through the fixed atoms dialog box? Also, does anyone
> have a keybinding for "Clear Fixed Atoms"?
>
> Thanks!
>
> -Sam
>
>

Re: [ccp4bb] Coot keybinding for fixing an atom in place

[Paul Emsley]

There is no easy way to do this.

Both active-residue and closest-atom return the CA of a residue if a CA 
exists in the residue.  Most of the time that is a reasonable thing to 
do.  Not here though :-(


Paul.


On 10/12/12 19:05, Sam Stampfer wrote:
Thanks for your help! That is close, but it will only fix the alpha 
carbon of the selected residues.


On Mon, Dec 10, 2012 at 1:11 PM, Debreczeni, Judit 
> wrote:


off the top of my head (i.e. not tested):

(add-key-binding "fix atom" "F"

(lambda () (mark-atom-as-fixed (car (active-residue)) (cdr
(active-residue)) 1)))

(add-key-binding "clear fixed atoms" "D"

   (lambda () (clear-fixed-atoms-all)))


*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
] *On Behalf Of *Sam Stampfer
*Sent:* 10 December 2012 16:22
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] Coot keybinding for fixing an atom in place

Dear CCP4 Bulletin Board,

Does anyone have a keybinding I can add to my .coot file so that I
can hit a key (for example, Shift-F) to fix in place the actively
selected atom, without having to go through the fixed atoms dialog
box? Also, does anyone have a keybinding for "Clear Fixed Atoms"?

Thanks!

-Sam

[ccp4bb] CCP4 6.3.0 update 010

[eugene . krissinel]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

* QtRView: A new results viewer with graphs and launchers for Coot, CCP4MG and 
ViewHKL
* Nautilus: Added a missing template pdb-file
* Hgen: Bug fix in task interface
* Acorn: Bug fix in task interface
* Crank: Bug fix in ctruncate plugin
* Monomer Library: Several entries manually curated

The easiest way to obtain the update is to install the CCP4 update client, if 
you have not done so already. Details on how to install the CCP4 Update Manager 
are available from:

http://www.ccp4.ac.uk/download/update_manual.html

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.uk.

Many thanks for using CCP4,

Eugene Krissinel & Andrey Lebedev



-- 
Scanned by iCritical.

[ccp4bb] Inconsistency in Cell Dimensions - replacing old:

[Edward A. Berry]

I am experimenting with ALMN cross-rotation using some old known structures.
I was surprised to see what seems to be a requirement for the cell dimensions
of the two crystals to be the same. Is that the case?
Excerpts from the log follow.
eab

 Data line--- CROSS 5 30
. ..
 OPENED INPUT MTZ FILE
 Logical Name: HKLIN   Filename: /a/denzo/als060729/azx02/chbc1azx02r12.mtz
. . .
 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
  170.1490  181.3120  240.5010   90.   90.   90.
. . .
 OPENED INPUT MTZ FILE
 Logical Name: HKLIN2   Filename: /a/denzo/ant101master/ant101_complete.mtz
. . .
 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
  128.7980  168.5290  231.6520   90.   90.   90.
. . .
 Inconsistency in Cell Dimensions - replacing old:
 Old cell:170.14900 181.31200 240.50101  90.0  90.0  90.0
 New cell:128.79800 168.52901 231.65199  90.0  90.0  90.0

If it is really changing the cell parameters of one of the datasets,
won't that distort the patterson and interfere with correlation?
Am I doing something wrong?
The two files are specified as HKLIN and HKLIN2

[ccp4bb] Postdoctoral position in GPCR structural biology

[Pioszak, Augen A (HSC)]

An NIH-funded postdoctoral position in GPCR structural biology is available in 
the Pioszak laboratory in the Department of Biochemistry and Molecular Biology 
at the University of Oklahoma Health Sciences Center 
(http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/augen-pioszak-ph-d-).
  Projects involve structure/function studies of soluble domains of GPCRs as 
well as full-length receptors.

The Pioszak lab is housed in the modern S.L. Young Biomedical Research Center 
on the expanding medical school campus adjacent to the vibrant downtown 
Oklahoma City area.  We have state-of-the-art equipment for protein expression 
and purification, biophysical characterization of proteins (ITC, DSC, CD), 
robotic crystallization (ARI Gryphon), and in house X-ray data collection 
(Rigaku), as well as access to macromolecular crystallography beamlines at the 
APS synchrotron.

Applicants should hold a recent Ph.D. in Biochemistry or related area.  
Experience with molecular biology techniques, protein expression and 
purification, protein-protein interaction methodologies, and X-ray 
crystallography would be an advantage.  Experience with glycoproteins and/or 
membrane proteins is desired, but is not required.  Strong motivation and a 
strong work ethic are a must.

To apply, please send a cover letter describing your interest in the position 
and previous experience, CV, and the names and contact information for 3 
references to augen-pios...@ouhsc.edu.

Best Regards,

Augie Pioszak

-
Augen A. Pioszak, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center

Letter address (office):
975 N.E. 10th Street, BRC 462B  
P.O. Box 26901  
Oklahoma City, OK  73126-0901

Shipping address (lab):
975 N.E. 10th Street, BRC 464
Oklahoma City, OK  73104

Phone:  405-271-2401Fax:  405-271-3910  
Email:  augen-pios...@ouhsc.edu
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/augen-pioszak-ph-d-
-

[ccp4bb] How to merge data from 2 separate sections of same crystal

[Yuri Pompeu]

hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are 
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from Mosflm when I scale them?
Attempts to process them in the same session keep maling the program crash!
Thank you very much

Re: [ccp4bb] How to merge data from 2 separate sections of same crystal

[Ed Pozharski]

On 12/10/2012 08:45 PM, Yuri Pompeu wrote:

hello everyone,
I have collected data on a problematic crystal. (first mistake...)
Images spanning phi angles 45-80 look ok and usable, also images 229-279 are 
usable (index well and merge well too).
How can I combine the 2 separate .mtz files from Mosflm when I scale them?
Attempts to process them in the same session keep maling the program crash!
Thank you very much
Did you try the 85 frames to mosflm in one session (maybe move bad files 
away from the current folder for a clean try).


--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] How to merge data from 2 separate sections of same crystal

[Yuri Pompeu]

Thanks for all the suggestions on and off BB.
I used the GUI Sort/Reindex to combine 6 sections then ran Pointless and Scala.
Got a data set to 2.6A Rmerge 0.12 (0.06 inner shell) and solved it in C2221.
It is a good night!
Cheers,