[ccp4bb] Fully funded PhD studentship (UK fees)

[Laura Spagnolo]

A fully funded PhD studentship is available jointly between Dr Laura Spagnolo 
at the University of Edinburgh and Dr Daniel Myatt at the ISIS UK neutron 
source, to work on protein/nucleic acid complexes involved in genome regulation.

 

The student will have an opportunity to receive training in electron 
microscopy, small angle scattering, biochemical and biophysical 
characterization, with access to state of the art facilities at the University 
of Edinburgh and at the Rutherford Appleton Laboratories (near Oxford), and 
will contribute to advancing our knowledge of an important, recently discovered 
biological mechanism.

 

Please contact Dr Spagnolo (laura.spagn...@ed.ac.uk 
) for enquiries on the project and on how to 
apply.

 

Funding is in place for 4 years, covering UK fees.



Dr Laura Spagnolo
Institute of Structural Molecular Biology
University of Edinburgh
Room 506, Darwin Building 
King's Buildings Campus
Edinburgh EH9 3JR
United Kingdom
T: +44 (0)131 650 7066 
F: +44 (0)131 650 8650 
http://www.biology.ed.ac.uk/research/institutes/structure/homepage.php?id=lspagnolo
laura.spagn...@ed.ac.uk









The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[ccp4bb] Second RéNaFoBiS workshop on Integrative Structural Biology, June 5-12, 2015, Oléron, France

[Dominique HOUSSET]

Dear all,

There are still some spots available to attend  the *second RéNaFoBiS 
workshop*, dedicated to Integrative Structural Biology, that will take 
place on the *Oléron island (France), from June 5 to June 12, 2015*. The 
main objective of this workshop is to offer a theoritical and practical 
training in the different techniques used in integrative structural 
biology (X-ray diffraction, Small angle X-ray scattering, NMR, 
cryo-electron microscopy, cellular and molecular imaging, biophysical 
methods and macromolecular interactions.) The goals are to explain and 
illustrate, to an audience mainly composed of PhD students and young 
researchers, the contributions and limitations of each method with a 
strong emphasis on their complementarity and future developments.


The official language of the workshop is French but presentations may be 
given in English, depending on the overall profile of the students. For 
practicals, english and french speaking groups will be organised. Thus, 
not feeling very confortable with french language, should not deter you 
from registering!


*Registration is open on the web site:*
http://ecolebios2015.sciencesconf.org/
*Deadline for registration:* April 12th, 2015 (maximum number of 
participants: 25)
More information on the French Initiative ReNaFoBiS : 
http://www.renafobis.fr/


best regards,

Dominique Housset, on the behalf of RéNaFoBiS

--

Dominique HOUSSET


 Groupe IRPAS (Immune response to pathogens and altered self)

 Institut de Biologie Structurale
 71 avenue des Martyrs
 CS 10090
 38044 Grenoble Cedex 9 - France


 Tel.: (33) (0)4 57 42 86 18
 e-mail: dominique.hous...@ibs.fr
 web psb: http://www.psb-grenoble.eu
 web ibs: http://www.ibs.fr

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Harry Powell]

Hi Jacob

I noticed that there's no backstop shadow that might give a clue as to the 
direct beam position.

Do you know what wavelength radiation was used to bake this?

On 1 Apr 2015, at 12:03, Keller, Jacob wrote:

> Can anyone index this? It's got mostly split spots and a strange diffuse 
> scattering background
> 
> JPK
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
> 
> 
> 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Adrian Goldman]

no, and that’s why they all needed to be stored at Diamond in case future 
generations have better programs.  And this applies also to those that have 
already been digested - I mean, processed.

Adrian


On 01 Apr 2015, at 12:03, Keller, Jacob  wrote:

> Can anyone index this? It's got mostly split spots and a strange diffuse 
> scattering background
> 
> JPK
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
> 
> 
> 



signature.asc
Description: Message signed with OpenPGP using GPGMail

[ccp4bb] European Crystallographic Computing School 20-22/8/2015 in Croatia

[Andrea Thorn]

We would like to announce the

European Crystallographic Computing School:
Advanced Software Development for Crystallographers
from the 20th to 22nd August 2015 in Duga Uvala, Croatia.

Location: Hotel Croatia at the beach location Duga Uvala, Croatia, 40 
kms from Rovinj

Cost: 100 € including full board, excluding accommodation.
(Bursaries are available.)
More infos and registration:   http://sig9.ecanews.org/rovinj.html

This School for active and future software developers will cover 
advanced topics in the design of crystallographic programs. We will 
focus on tutorials in small groups, with plenary lectures covering 
aspects relevant to all crystallographic disciplines. We will also 
provide opportunity for one-on-one problem solving sessions as well as 
networking, integrating new developers into the crystallographic 
software community. Participants are invited to contribute tutorials.
The School is organized by the Crystallographic Computing Special 
Interest Group (ECACOMSIG) as a satellite meeting to the European 
Crystallographic Meeting (ECM29) in Rovinj. All queries should be sent 
to Harry Powell (ha...@mrc-lmb.cam.ac.uk) or Andrea Thorn 
(ath...@mrc-lmb.cam.ac.uk).


Confirmed speakers include:
•Luc Bourhis, Paris, France
•Kay Diederichs, Konstanz, Germany
•Eleanor Dodson, York, UK
•Vincent Favre-Nicolin, Grenoble, France
•Christian Jelsch, France
•Anders Madsen, Copenhagen, Denmark
•Santosh Panjikar, Melbourne, Australia
•Harry Powell, Cambridge, UK
•Andrea Thorn, Cambridge, UK
•George Sheldrick, Goettingen, Germany

The school is kindly sponsored by CCP4, Dectris, Agilent Technologies 
and Bruker AXS.


--
Dr. Andrea Thorn
Secretary of ECA SIG9 (Crystallographic Computing)

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Julia Griese]

This one appears to be of a similar age. It has a most puzzling, but 
pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't 
appear to support the image format.


/Julia



On 01/04/15 13:08, Harry Powell wrote:

Hi Jacob

I noticed that there's no backstop shadow that might give a clue as to 
the direct beam position.


Do you know what wavelength radiation was used to bake this?

On 1 Apr 2015, at 12:03, Keller, Jacob wrote:

Can anyone index this? It's got mostly split spots and a strange 
diffuse scattering background


JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org 
***





Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick 
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 
(Crystallographic Computing)













--
Dr. Julia Griese
Postdoctoral Researcher
Stockholm Center for Biomembrane Research
Department of Biochemistry and Biophysics
Stockholm University
106 91 Stockholm
Sweden

phone: +46-(0)8-162 778
email: gri...@dbb.su.se

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Gloria Borgstahl]

Ah Ha!

drum roll

A quasicrystal   !

On Wed, Apr 1, 2015 at 7:00 AM, Julia Griese  wrote:

>  This one appears to be of a similar age. It has a most puzzling, but
> pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't
> appear to support the image format.
>
> /Julia
>
>
>
> On 01/04/15 13:08, Harry Powell wrote:
>
> Hi Jacob
>
>  I noticed that there's no backstop shadow that might give a clue as to
> the direct beam position.
>
>  Do you know what wavelength radiation was used to bake this?
>
>  On 1 Apr 2015, at 12:03, Keller, Jacob wrote:
>
>  Can anyone index this? It's got mostly split spots and a strange diffuse
> scattering background
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>
>
> 
>
>
>Harry
> --
>Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis
> Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
> Chairman of International Union of Crystallography Commission on
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
>
>
>
>
>
>
>
>
>
>
> --
> Dr. Julia Griese
> Postdoctoral Researcher
> Stockholm Center for Biomembrane Research
> Department of Biochemistry and Biophysics
> Stockholm University
> 106 91 Stockholm
> Sweden
>
> phone: +46-(0)8-162 778
> email: gri...@dbb.su.se
>
>

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Finke Aaron (PSI)]

--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch

On Apr 1, 2015, at 13:03, Keller, Jacob  wrote:

> Can anyone index this? It's got mostly split spots and a strange diffuse 
> scattering background
> 
> JPK
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
> 
> 
> 

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[H. Raaijmakers]

Have you tried Shake-and-Bake? An old program, but works great when you
have mixed real and reciprocal space cake.

Keller, Jacob schreef:
> Can anyone index this? It's got mostly split spots and a strange diffuse
> scattering background
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>
>
>

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Helena Taberman]

I think we used the same version of Mosflm when we managed to solve this 
strange pattern.

[cid:4EF3709E-41D5-4A38-8CE9-064D75929422@uefad.uef.fi]


Helena Taberman, M.Sc.

University of Eastern Finland
Department of Chemistry
Joensuu Campus
P.O. Box 111
FI-80101 Joensuu, FINLAND

Mobile: +358 50 337 2488


Finke Aaron (PSI) mailto:aaron.fi...@psi.ch>> kirjoitti 
1.4.2015 kello 15.27:

I have seen this before, actually. It appears to be multiple lattices, but if 
you carefully index it with Loxflm (a less well-known version of Mosflm), I was 
able to get a solution from bagelecular replacement:

 

Note that the sesame seeds are disordered.

Hope that helps,
Aaron
--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch

On Apr 1, 2015, at 13:03, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

Can anyone index this? It's got mostly split spots and a strange diffuse 
scattering background

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Folmer Fredslund]

Hi Julia,

This was clearly taken at MAXlab, since it's a very distinct Swedish
pattern. I would guess I911-2, unless of course it is a very old one from
I711.
There was a problem once, where the header of the file didn't get written
correctly.

Can you index it if you manually guess the beam position (somewhere behind
the beamstop) and input it to imosflm? It should work, although you might
have to try a number of guesses, seing the beamstop is so big.

HTH,
Folmer

2015-04-01 14:00 GMT+02:00 Julia Griese :

>  This one appears to be of a similar age. It has a most puzzling, but
> pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't
> appear to support the image format.
>
> /Julia
>
>
>
> On 01/04/15 13:08, Harry Powell wrote:
>
> Hi Jacob
>
>  I noticed that there's no backstop shadow that might give a clue as to
> the direct beam position.
>
>  Do you know what wavelength radiation was used to bake this?
>
>  On 1 Apr 2015, at 12:03, Keller, Jacob wrote:
>
>  Can anyone index this? It's got mostly split spots and a strange diffuse
> scattering background
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>
>
> 
>
>
>Harry
> --
>Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis
> Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
> Chairman of International Union of Crystallography Commission on
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
>
>
>
>
>
>
>
>
>
>
> --
> Dr. Julia Griese
> Postdoctoral Researcher
> Stockholm Center for Biomembrane Research
> Department of Biochemistry and Biophysics
> Stockholm University
> 106 91 Stockholm
> Sweden
>
> phone: +46-(0)8-162 778
> email: gri...@dbb.su.se
>
>


-- 
Folmer Fredslund

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[David Briggs]

This looks like a tough cookie.

IMO you'd be crackers to persist with this crystal form. It's certainly not
going to be a piece of cake.

Dr David C Briggs PhD
http://about.me/david_briggs
On 1 Apr 2015 12:07, "Keller, Jacob"  wrote:

> Can anyone index this? It's got mostly split spots and a strange diffuse
> scattering background
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>
>
>

[ccp4bb] No MR solution

[Sekharreddy M]

HI All,
  I am trying to find MR solution for one of the protein crystals
with 3.0A resolution, but not able find solution using Phaser (PHENIX).The
protein has two domains.and the probable best space group identified was
p4212(HKL2000).

 I am novice in using crystallization tools for solving structures.I am
stuck at this stage  and I appreciate any help in this regard.

Thank you.

Re: [ccp4bb] No MR solution

[Roger Rowlett]

There are 8 possible space groups in the P422 family. Did you search in all
of these? How many search models are likely to fit in the unit cell based
on  Matthews analysis? Then there are questions about model selection and
preparation. How identical is the search model to the target? Does it make
sense to search for the domains separately? Did you truncate the model side
chains?

There are lots of ways to skin the cat depending on the problems
encountered. 3.0 A may be challenging for a low identity search model.

__
Roger Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
On Apr 1, 2015 11:06 AM, "Sekharreddy M"  wrote:

> HI All,
>   I am trying to find MR solution for one of the protein crystals
> with 3.0A resolution, but not able find solution using Phaser (PHENIX).The
> protein has two domains.and the probable best space group identified was
> p4212(HKL2000).
>
>  I am novice in using crystallization tools for solving structures.I am
> stuck at this stage  and I appreciate any help in this regard.
>
> Thank you.
>

[ccp4bb] Number of Molecules in Asymetric Unit

[amro selem]

Dear CCP4 Community ,which program i should use in ccp4 backage to find how 
many molecules in Asymetric Unit .All the bestAmr
 

Re: [ccp4bb] Number of Molecules in Asymetric Unit

[Roger Rowlett]

In the CCP4i GUI you will find "Phaser Cell Content Analysis" under the 
"Analysis" tab. IIRC, this calls up the Matthews Probability Calculator. 
It will give you a good idea of the likely number of search models in 
the ASU. For large numbers, e.g. >3, the most probable number is likely 
to be unreliable and you might try smaller numbers and observing the 
packing of the partial solutions to get a better clue of the correct number.


Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 4/1/2015 11:45 AM, amro selem wrote:

Dear CCP4 Community ,
which program i should use in ccp4 backage to find how many molecules 
in Asymetric Unit .

All the best
Amr

Re: [ccp4bb] Number of Molecules in Asymetric Unit

[doris quay]

It's the Mathews Coefficient. 


 On Wednesday, April 1, 2015 4:51 PM, amro selem 
<03391c09f749-dmarc-requ...@jiscmail.ac.uk> wrote:
   

 Dear CCP4 Community ,which program i should use in ccp4 backage to find how 
many molecules in Asymetric Unit .All the bestAmr
 

   

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Derek Logan]

These last puns just take the biscuit!
Derek

On 1 Apr 2015, at 16:52, David Briggs 
mailto:drdavidcbri...@gmail.com>> wrote:


This looks like a tough cookie.

IMO you'd be crackers to persist with this crystal form. It's certainly not 
going to be a piece of cake.


Dr David C Briggs PhD
http://about.me/david_briggs

On 1 Apr 2015 12:07, "Keller, Jacob" 
mailto:kell...@janelia.hhmi.org>> wrote:
Can anyone index this? It's got mostly split spots and a strange diffuse 
scattering background

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] No MR solution

[David Schuller]

On 04/01/15 11:23, Roger Rowlett wrote:


There are 8 possible space groups in the P422 family. Did you search 
in all of these?


What he said. The answer should be "YES". Phaser is set up to do this 
easily.


How many search models are likely to fit in the unit cell based on  
Matthews analysis? Then there are questions about model selection and 
preparation. How identical is the search model to the target? Does it 
make sense to search for the domains separately?


If the domains are separate enough to be called "domains", it might be 
worthwhile to try this.


Did you truncate the model side chains?

I usually try with the full sequence, and with a poly-Ala truncation. 
Especially if the sequence identity between model and target is low.


BTW, you didn't mention anything about the similarity or identity of the 
model. That's important in figuring out whether you should have been 
successful or not. Much more so than the resolution of the data.


There are lots of ways to skin the cat depending on the problems 
encountered. 3.0 A may be challenging for a low identity search model.


__
Roger Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University

On Apr 1, 2015 11:06 AM, "Sekharreddy M" > wrote:


HI All,
  I am trying to find MR solution for one of the protein
crystals with 3.0A resolution, but not able find solution using
Phaser (PHENIX).The protein has two domains.and the probable best
space group identified was p4212(HKL2000).

 I am novice in using crystallization tools for solving
structures.I am stuck at this stage  and I appreciate any help in
this regard.

Thank you.




--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] Number of Molecules in Asymetric Unit

[Bernhard Rupp (Hofkristallrat a.D.)]

New kernel version

 

  
http://www.ruppweb.org/mattprob/default.html

 

Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of amro selem
Sent: Wednesday, April 01, 2015 8:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Number of Molecules in Asymetric Unit

 

Dear CCP4 Community ,

which program i should use in ccp4 backage to find how many molecules in 
Asymetric Unit .

All the best

Amr

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Marjolein Thunnissen]

Working at the MAX IV Laboratory (as it is called these days) I can indeed 
confirm it is a Swedish pattern, but I have not yet found a trace of the data 
itself, so I am not so sure it was collected here...

However, as we will open the brightest synchrotron source in the world next 
year, we can offer beam time and assistance to solve this problem, maybe a good 
day to test this further  would be 1-4-2017

best regards

Marjolein




On 01 Apr 2015, at 16:01, Folmer Fredslund 
mailto:folm...@gmail.com>> wrote:

Hi Julia,

This was clearly taken at MAXlab, since it's a very distinct Swedish pattern. I 
would guess I911-2, unless of course it is a very old one from I711.
There was a problem once, where the header of the file didn't get written 
correctly.

Can you index it if you manually guess the beam position (somewhere behind the 
beamstop) and input it to imosflm? It should work, although you might have to 
try a number of guesses, seing the beamstop is so big.

HTH,
Folmer

2015-04-01 14:00 GMT+02:00 Julia Griese 
mailto:gri...@dbb.su.se>>:
This one appears to be of a similar age. It has a most puzzling, but pretty 
pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't appear to 
support the image format.

/Julia




On 01/04/15 13:08, Harry Powell wrote:
Hi Jacob

I noticed that there's no backstop shadow that might give a clue as to the 
direct beam position.

Do you know what wavelength radiation was used to bake this?

On 1 Apr 2015, at 12:03, Keller, Jacob wrote:

Can anyone index this? It's got mostly split spots and a strange diffuse 
scattering background

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)












--
Dr. Julia Griese
Postdoctoral Researcher
Stockholm Center for Biomembrane Research
Department of Biochemistry and Biophysics
Stockholm University
106 91 Stockholm
Sweden

phone: +46-(0)8-162 778
email: gri...@dbb.su.se




--
Folmer Fredslund

[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]




Dr. Marjolein Thunnissen
Science Coordinator Structural Biology

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Ole Römers väg 1, 223 63 Lund
Telephone: +46 766 32 04 17
www.maxlab.lu.se

[ccp4bb] Postdoctoral Position studying complement-like immunity in mosquitoes

[Richard Baxter]

A postdoctoral position is available in the laboratory of Prof. Richard
Baxter at Yale University (baxterlab.yale.edu). The successful candidate
will address structural and mechanistic questions regarding the innate
immune response of the malaria vector *Anopheles gambiae*. They will join a
research group that combines biophysical techniques such as x-ray
crystallography, small-angle x-ray scattering with biochemistry, chemical
and cell biology. The laboratory is located in the Kline Chemistry
Laboratory (newly renovated June 2014) with access to in-house x-ray
diffraction and biophysical instrumentation, cryo-EM facility and expanding
facilities for proteomics and high-throughput biology at the Yale Keck
Center and the Yale West Campus.


A PhD in chemistry, biochemistry, biophysics or other relevant discipline
is required. Experience with macromolecular crystallography, SAXS, electron
microscopy or mass spectrometry is preferred, experience in vector biology
or host-pathogen interactions is a plus.


Interested applicants please submit a cover letter, resume and contact
information for three references to Richard Baxter, Tel: +1 203 432 9576,
225 Prospect Street, PO Box 208107, New Haven CT 06511, or email
richard.bax...@yale.edu

Re: [ccp4bb] nVidia quadro

[Kay Diederichs]

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
 wrote:

>On 3/25/2015 18:10, Kay Diederichs wrote:
>> On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  
>> wrote:
>>
>>> You could check the nVidia page of officially supported displays. It
>>> includes a search tab so you can check for "Built-in Emitter."
>>> http://www.nvidia.com/object/3d-vision-displays.html
>>>
>>> Performing that search brings up 5 contenders. Good luck finding any of
>>> these products still for sale.
>> Unfortunately, this NVidia page has not been updated for years.
>>
>> The qualifier "3D-fähig (aktiv)" at 
>> http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top
>>  should indicate a built-in emitter, but I looked at some of the 
>> descriptions of these 11 monitors and was unable to confirm that they indeed 
>> have a built-in emitter. So one has to research every specific case.
>>
>> I changed the wording on the wiki page.
>>
>> Kay
>>
>I went through the specs for the monitors on the Heise list, and none of
>them seems to have a built in emitter compatible with Nvidia 3D Vision
>2. It looks like it is a bad time to buy a 3D monitor. At this point it
>might be easier to just go for a Quadro with 3-pin connector.
>
>Best,
>Andreas
>

I asked the company who runs the price info site to check their assignments, 
and they fixed the categories: http://geizhals.eu/?cat=monlcd19wide now has a 
"inkl. 3D-emitter" attribute. This currently only returns the Asus 278HR which 
can only be bought in Poland, or through EBay.

The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo connector 
(needed for Linux) is the K4200 
(http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at 
~ €700.

best,

Kay

Re: [ccp4bb] nVidia quadro

[Lukasz Salwinski]

On 04/01/2015 12:31 PM, Kay Diederichs wrote:

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
 wrote:


On 3/25/2015 18:10, Kay Diederichs wrote:

On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  wrote:


You could check the nVidia page of officially supported displays. It
includes a search tab so you can check for "Built-in Emitter."
http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any of
these products still for sale.

Unfortunately, this NVidia page has not been updated for years.

The qualifier "3D-fähig (aktiv)" at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top 
should indicate a built-in emitter, but I looked at some of the descriptions of these 11 
monitors and was unable to confirm that they indeed have a built-in emitter. So one has to 
research every specific case.

I changed the wording on the wiki page.

Kay


I went through the specs for the monitors on the Heise list, and none of
them seems to have a built in emitter compatible with Nvidia 3D Vision
2. It looks like it is a bad time to buy a 3D monitor. At this point it
might be easier to just go for a Quadro with 3-pin connector.

Best,
Andreas



I asked the company who runs the price info site to check their assignments, and they 
fixed the categories: http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 
3D-emitter" attribute. This currently only returns the Asus 278HR which can only be 
bought in Poland, or through EBay.

The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo connector 
(needed for Linux) is the K4200 
(http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at 
~ €700.

best,

Kay


FX3700 is the oldest Quadro model with 3-pin DIN Stereo connector that is
supported by the current nvidia drivers. it can be bought on ebay
for about $30-$40. works fine with coot/pymol.

lukasz


--
-
 Lukasz Salwinski PHONE:310-825-1402
 UCLA-DOE Institute for Genomics & Proteomics   FAX:310-206-3914
 UCLA, Los AngelesEMAIL: luk...@mbi.ucla.edu
-

[ccp4bb] Sortwater NCS Matrix input

[Shane Caldwell]

Hi ccp4bb,

I'm trying to solve a problem I never quite figured out in the past. I'd
like to use the *sortwater* utility to send my picked waters to various
protein chains, and to give them the same residue number if they are
NCS-equivalent, as the manual outlines.

http://www.ccp4.ac.uk/html/sortwater.html

The first part goes off perfectly, partitioning the waters into their
respective chains. Where I run into problems is bringing in NCS. I can't
get the program to recognize the transformation matrix. I can calculate the
matrix using *superpose*, and manually input these (limited precision)
values into my script, which looks like:

NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004 -0.994
37.502 -35.283 81.276

and it returns

 WARNING:   Matrix is not orthonormal 


My linear algebra is very limited, and I don't know exactly what this means
in the context of this program, though I suspect it could be either linked
to converting to fractional coordinates (I'm in a monoclinic system), or a
product of the limited precision of the matrix values.

Using the identity matrix, like so:

NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0
0.0 1.0 0.000 0.000 0.000

doesn't trigger the warning. These values have more digits, but adding
extra zeroes to the original matrix as a very crude workaround still
returns the error.

So, I'm now stuck trying to parse what's going on. I know *sortwater* also
takes O datablocks as matrix input, and that's something I could look into
(especially if calculating in a different program might get me better
precision). Although, I'm not sure the format is a factor given the
identity matrix is accepted as a keyword input.

Skimming the archives, I get the sense this isn't something that many users
do any more. I have quite a few structures with hundreds of waters each and
I'd like to get the waters organized, but doing it by hand will take a very
long time. Any help getting this program running would be greatly
appreciated!


Shane Caldwell
McGill University

Re: [ccp4bb] nVidia quadro

[Andreas Schenk]

Thank you Kay for contacting the info site. The new categories are 
definitely more helpful.

And thank  you Lukasz, for the info about the FX3700.

Best,
Andreas

On 04/01/2015 03:57 PM, Lukasz Salwinski wrote:

On 04/01/2015 12:31 PM, Kay Diederichs wrote:

On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
 wrote:


On 3/25/2015 18:10, Kay Diederichs wrote:

On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  wrote:


You could check the nVidia page of officially supported displays. It
includes a search tab so you can check for "Built-in Emitter."
http://www.nvidia.com/object/3d-vision-displays.html

Performing that search brings up 5 contenders. Good luck finding any of
these products still for sale.

Unfortunately, this NVidia page has not been updated for years.

The qualifier "3D-fähig (aktiv)" at 
http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top 
should indicate a built-in emitter, but I looked at some of the descriptions of these 11 
monitors and was unable to confirm that they indeed have a built-in emitter. So one has to 
research every specific case.

I changed the wording on the wiki page.

Kay


I went through the specs for the monitors on the Heise list, and none of
them seems to have a built in emitter compatible with Nvidia 3D Vision
2. It looks like it is a bad time to buy a 3D monitor. At this point it
might be easier to just go for a Quadro with 3-pin connector.

Best,
Andreas


I asked the company who runs the price info site to check their assignments, and they 
fixed the categories: http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 
3D-emitter" attribute. This currently only returns the Asus 278HR which can only be 
bought in Poland, or through EBay.

The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo connector 
(needed for Linux) is the K4200 
(http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts at 
~ €700.

best,

Kay

FX3700 is the oldest Quadro model with 3-pin DIN Stereo connector that is
supported by the current nvidia drivers. it can be bought on ebay
for about $30-$40. works fine with coot/pymol.

lukasz

Re: [ccp4bb] Sortwater NCS Matrix input

[Dale Tronrud]

   I think you are on the right track - There are not enough decimal
points in your matrix elements to pass the orthonormal test.  This test
checks that the length of each row (x^2+y^2+z^2) is equal to one and the
dot product of each row with every other row is equal to zero.  If the
values on your NCS statement are in row order I calculate 0.999337 for
the length of the first row.  If the program is testing if this is equal
to one to four decimal points you lose.

   You have to add more digits, but just adding zeros isn't going to
accomplish much.  The best solution is to get your ncs program to report
its matrix with more digits -- three is pitiful.  Failing that you could
calculate one element of each row from the other two to ensure the
length is equal to one at a higher level of precision and hope this
doesn't mess up the dot product test.  You'll end up with one number in
each row having more than three decimal places.

Dale Tronrud

On 4/1/2015 2:52 PM, Shane Caldwell wrote:
> Hi ccp4bb,
> 
> I'm trying to solve a problem I never quite figured out in the past. I'd
> like to use the *sortwater* utility to send my picked waters to various
> protein chains, and to give them the same residue number if they are
> NCS-equivalent, as the manual outlines.
> 
> http://www.ccp4.ac.uk/html/sortwater.html
> 
> The first part goes off perfectly, partitioning the waters into their
> respective chains. Where I run into problems is bringing in NCS. I can't
> get the program to recognize the transformation matrix. I can calculate
> the matrix using *superpose*, and manually input these (limited
> precision) values into my script, which looks like:
> 
> NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004
> -0.994 37.502 -35.283 81.276
> 
> and it returns
> 
>  WARNING:   Matrix is not orthonormal 
> 
> 
> My linear algebra is very limited, and I don't know exactly what this
> means in the context of this program, though I suspect it could be
> either linked to converting to fractional coordinates (I'm in a
> monoclinic system), or a product of the limited precision of the matrix
> values.
> 
> Using the identity matrix, like so:
> 
> NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0
> 0.0 1.0 0.000 0.000 0.000
> 
> doesn't trigger the warning. These values have more digits, but adding
> extra zeroes to the original matrix as a very crude workaround still
> returns the error.
> 
> So, I'm now stuck trying to parse what's going on. I know *sortwater*
> also takes O datablocks as matrix input, and that's something I could
> look into (especially if calculating in a different program might get me
> better precision). Although, I'm not sure the format is a factor given
> the identity matrix is accepted as a keyword input.
> 
> Skimming the archives, I get the sense this isn't something that many
> users do any more. I have quite a few structures with hundreds of waters
> each and I'd like to get the waters organized, but doing it by hand will
> take a very long time. Any help getting this program running would be
> greatly appreciated!
> 
> 
> Shane Caldwell
> McGill University

[ccp4bb] strange pattern

[Gert Vriend]

The following article was rejected by 'our' journal...

http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/april_fools__day_special_papers.htm 



Greetings
Gert

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Andrea Thorn]

These diffraction patterns, called "matzo" (Hebrew: מַצָּה‎) have been 
observed already by the ancient jews, and it is thought that the 
invention of the millstone (see http://galleryhip.com/millstone.html) is 
a consequence of early detector technology to produce these images.


Andrea.

On 01/04/2015 12:03, Keller, Jacob wrote:

Can anyone index this? It's got mostly split spots and a strange diffuse 
scattering background

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***




--
Dr Andrea Thorn
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
   andrea.th...@web.de
http://shelx.uni-ac.gwdg.de/~athorn

Re: [ccp4bb] Sortwater NCS Matrix input

[Shane Caldwell]

Alright, thanks! It's a good thing, then, I spent the afternoon brushing up
on matrices.

I guess the next, probably more general question for the bb is: which
utilities export an NCS transformation matrix with more precision?
*superpose* and *gesamt* only export three decimals, though I'm sure they
use greater precision under the hood. I'm not opposed to exporting from
coot or pymol either, I just haven't figured out how to do this yet - what
would be the simplest way to calculate and export an NCS transformation
matrix?

Shane

On Wed, Apr 1, 2015 at 7:34 PM, Dale Tronrud  wrote:

>
>I think you are on the right track - There are not enough decimal
> points in your matrix elements to pass the orthonormal test.  This test
> checks that the length of each row (x^2+y^2+z^2) is equal to one and the
> dot product of each row with every other row is equal to zero.  If the
> values on your NCS statement are in row order I calculate 0.999337 for
> the length of the first row.  If the program is testing if this is equal
> to one to four decimal points you lose.
>
>You have to add more digits, but just adding zeros isn't going to
> accomplish much.  The best solution is to get your ncs program to report
> its matrix with more digits -- three is pitiful.  Failing that you could
> calculate one element of each row from the other two to ensure the
> length is equal to one at a higher level of precision and hope this
> doesn't mess up the dot product test.  You'll end up with one number in
> each row having more than three decimal places.
>
> Dale Tronrud
>
> On 4/1/2015 2:52 PM, Shane Caldwell wrote:
> > Hi ccp4bb,
> >
> > I'm trying to solve a problem I never quite figured out in the past. I'd
> > like to use the *sortwater* utility to send my picked waters to various
> > protein chains, and to give them the same residue number if they are
> > NCS-equivalent, as the manual outlines.
> >
> > http://www.ccp4.ac.uk/html/sortwater.html
> >
> > The first part goes off perfectly, partitioning the waters into their
> > respective chains. Where I run into problems is bringing in NCS. I can't
> > get the program to recognize the transformation matrix. I can calculate
> > the matrix using *superpose*, and manually input these (limited
> > precision) values into my script, which looks like:
> >
> > NCS B C MATRIX 0.072 0.997 -0.012 0.991 -0.073 -0.113 -0.113 -0.004
> > -0.994 37.502 -35.283 81.276
> >
> > and it returns
> >
> >  WARNING:   Matrix is not orthonormal 
> >
> >
> > My linear algebra is very limited, and I don't know exactly what this
> > means in the context of this program, though I suspect it could be
> > either linked to converting to fractional coordinates (I'm in a
> > monoclinic system), or a product of the limited precision of the matrix
> > values.
> >
> > Using the identity matrix, like so:
> >
> > NCS B C MATRIX 1.0 0.0 0.0 0.0 1.0 0.0 0.0
> > 0.0 1.0 0.000 0.000 0.000
> >
> > doesn't trigger the warning. These values have more digits, but adding
> > extra zeroes to the original matrix as a very crude workaround still
> > returns the error.
> >
> > So, I'm now stuck trying to parse what's going on. I know *sortwater*
> > also takes O datablocks as matrix input, and that's something I could
> > look into (especially if calculating in a different program might get me
> > better precision). Although, I'm not sure the format is a factor given
> > the identity matrix is accepted as a keyword input.
> >
> > Skimming the archives, I get the sense this isn't something that many
> > users do any more. I have quite a few structures with hundreds of waters
> > each and I'd like to get the waters organized, but doing it by hand will
> > take a very long time. Any help getting this program running would be
> > greatly appreciated!
> >
> >
> > Shane Caldwell
> > McGill University
>

Re: [ccp4bb] nVidia quadro

[Aidong Han]

Interestingly, we have both systems working in our lab. Our old station is 7 
years old with FX3700, view sonic monitor and 3-pin stereo emitter. My new one 
has K5000 and VG278HR, which just requires a pair of nVidia shatter glasses.  
Hope this helps.  Aidong

On Apr 2, 2015, at 7:20 AM, Andreas Schenk  
wrote:

> Thank you Kay for contacting the info site. The new categories are definitely 
> more helpful.
> And thank  you Lukasz, for the info about the FX3700.
> 
> Best,
> Andreas
> 
> On 04/01/2015 03:57 PM, Lukasz Salwinski wrote:
>> On 04/01/2015 12:31 PM, Kay Diederichs wrote:
>>> On Tue, 31 Mar 2015 15:04:31 -0400, Andreas Schenk 
>>>  wrote:
>>> 
 On 3/25/2015 18:10, Kay Diederichs wrote:
> On Wed, 25 Mar 2015 14:16:55 -0400, David Schuller  
> wrote:
> 
>> You could check the nVidia page of officially supported displays. It
>> includes a search tab so you can check for "Built-in Emitter."
>> http://www.nvidia.com/object/3d-vision-displays.html
>> 
>> Performing that search brings up 5 contenders. Good luck finding any of
>> these products still for sale.
> Unfortunately, this NVidia page has not been updated for years.
> 
> The qualifier "3D-fähig (aktiv)" at 
> http://www.heise.de/preisvergleich/?cat=monlcd19wide&xf=5848_3D-f%E4hig+(aktiv)#xf_top
>  should indicate a built-in emitter, but I looked at some of the 
> descriptions of these 11 monitors and was unable to confirm that they 
> indeed have a built-in emitter. So one has to research every specific 
> case.
> 
> I changed the wording on the wiki page.
> 
> Kay
> 
 I went through the specs for the monitors on the Heise list, and none of
 them seems to have a built in emitter compatible with Nvidia 3D Vision
 2. It looks like it is a bad time to buy a 3D monitor. At this point it
 might be easier to just go for a Quadro with 3-pin connector.
 
 Best,
 Andreas
 
>>> I asked the company who runs the price info site to check their 
>>> assignments, and they fixed the categories: 
>>> http://geizhals.eu/?cat=monlcd19wide now has a "inkl. 3D-emitter" 
>>> attribute. This currently only returns the Asus 278HR which can only be 
>>> bought in Poland, or through EBay.
>>> 
>>> The cheapest current Nvidia Quadro with (optional?) 3-pin DIN Stereo 
>>> connector (needed for Linux) is the K4200 
>>> (http://www.nvidia.de/object/quadro-desktop-gpu-specs-de.html) which starts 
>>> at ~ €700.
>>> 
>>> best,
>>> 
>>> Kay
>> FX3700 is the oldest Quadro model with 3-pin DIN Stereo connector that is
>> supported by the current nvidia drivers. it can be bought on ebay
>> for about $30-$40. works fine with coot/pymol.
>> 
>> lukasz
>> 
>> 

[ccp4bb] on building a helix fragment by coot

[Smith Liu]

Dear All,
 
Caused by poor resolution, I can only build a series of Ala into my helix 
density (for sure the density is for helix). Then I tried to use the dock 
sequence in the extension of the Coot to change to my target sequence. Coot 
says it was not confidence on the alignment, thus it did not change the Alas 
into my target sequence.
 
In the "Molecule to be sequenced" in the coot dock sequence, if we paste the 
sequence, show we still need to input the pir file? For the sequenc we paste, 
it should be my target sequence rather than the series of Alas , right? Why in 
this graphical interface there are "Sequence closest fragment" and "Sequnece 
all fragments!"?
 
I ask these questions in order to avoid my failling to do something which Coot 
can do.
 
I am looking forward to getting your reply.
 
Smith







 Forwarding messages 
From: "Smith Liu" 
Date: 2015-04-01 12:58:01
To: lists...@jiscmail.ac.uk,"CCP4BB@JISCMAIL.AC.UK" 
Subject: on building a helix fragment by coot

Dear All,
 
If I need to build a fragment of helix to a fragment of density by coot, should 
I use baton build method or should I use place Helix here function? I have 
tried both, but I find it is difficult to place the sidechains to the map 
mosition which looks like where shold be occupied by the sidechains.
 
I am looking forward to getting your message on how to correctly buld the helix.
 
Best regards.
 
Smith

Re: [ccp4bb] strange pattern

[Ethan Merritt]

On Thursday, 02 April 2015 02:21:48 AM Gert Vriend wrote:
> The following article was rejected by 'our' journal...
> 
> http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/april_fools__day_special_papers.htm
>  
> 

A most excellent contribution!

Do you have a refmac-compatible *.cif dictionary describing
the tetrahedral sulfur center as in 3d7s (Figure 3D)?
I would hate to miss one of these should I suspect the
opportunity for novel quantum chemistry in a structure 
being refined.

Ethan

 
> Greetings
> Gert

-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Jens Kaiser]

Gloria,
  I think this one might be modulated, you can clearly distinguish Bragg
and satellite reflections.

-j.


On Wed, 2015-04-01 at 07:06 -0500, Gloria Borgstahl wrote:
> Ah Ha!  
> 
> 
> drum roll
> 
> 
> A quasicrystal   !
> 
> On Wed, Apr 1, 2015 at 7:00 AM, Julia Griese  wrote:
> This one appears to be of a similar age. It has a most
> puzzling, but pretty pentagonal pattern (and a backstop).
> Unfortunately Mosflm doesn't appear to support the image
> format. 
> 
> /Julia
> 
> 
> 
> 
> On 01/04/15 13:08, Harry Powell wrote:
> 
> > Hi Jacob 
> > 
> > 
> > I noticed that there's no backstop shadow that might give a
> > clue as to the direct beam position. 
> > 
> > 
> > Do you know what wavelength radiation was used to bake this?
> > 
> > On 1 Apr 2015, at 12:03, Keller, Jacob wrote:
> > 
> > > Can anyone index this? It's got mostly split spots and a
> > > strange diffuse scattering background
> > > 
> > > JPK
> > > 
> > > ***
> > > Jacob Pearson Keller, PhD
> > > Looger Lab/HHMI Janelia Research Campus
> > > 19700 Helix Dr, Ashburn, VA 20147
> > > email: kell...@janelia.hhmi.org
> > > ***
> > > 
> > > 
> > > 
> > 
> > Harry
> > --
> > Dr Harry Powell, MRC Laboratory of Molecular Biology,
> > Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge
> > CB2 0QH
> > Chairman of International Union of Crystallography
> > Commission on Crystallographic Computing
> > Chairman of European Crystallographic Association SIG9
> > (Crystallographic Computing) 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> 
> 
> -- 
> Dr. Julia Griese
> Postdoctoral Researcher
> Stockholm Center for Biomembrane Research
> Department of Biochemistry and Biophysics
> Stockholm University
> 106 91 Stockholm
> Sweden
> 
> phone: +46-(0)8-162 778
> email: gri...@dbb.su.se
> 
>