[ccp4bb] Bioimaging developer at EMBL-EBI

[Ardan Patwardhan]

Dear all

EMBL-EBI is embarking on a project to build a scalable (well into the the 100’s 
of petabytes and beyond) public archive for bioimaging data which will also 
become the back-end for EMPIAR  (empiar.org ). We are 
looking for a person with experience in developing software involving 2D/3D 
structural or imaging data to help build the software infrastructure 
interfacing with the bioimaging archive.
More details of the post can be found here: 
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01157=1 

Closing date: 18 March 2018

Best wishes


Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

Re: [ccp4bb] 3D Structure Search

[Ethan A Merritt]

On Thursday, February 15, 2018 3:16:50 PM PST Nicola Evans wrote:
> I have recently solved a novel structure which previously did not have any 
> structural homologues (as related by sequence identity). I was wondering if 
> anyone could recommend a 3D structural search engine? I used the Dali server 
> which has been recommended to me in the past (and with past success) but the 
> top few hits this time aren't similar structurally (although I haven't 
> exhausted the list yet). I just want to confirm if the folds are truly novel 
> or not.

Dali is sensitive to the order of secondary structure elements.
This is relevant if you are looking for evolutionary relatedness, but 
not if you just want to ask "does it look like this". 

For the latter question, I suggest the VAST server at NCBI.
https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] 3D Structure Search

[Tomas Malinauskas]

Dear Nicola,
PDBeFold is great too: http://www.ebi.ac.uk/msd-srv/ssm/
Best wishes,
Tomas

On Thu, Feb 15, 2018 at 11:16 PM, Nicola Evans  wrote:
> I have recently solved a novel structure which previously did not have any 
> structural homologues (as related by sequence identity). I was wondering if 
> anyone could recommend a 3D structural search engine? I used the Dali server 
> which has been recommended to me in the past (and with past success) but the 
> top few hits this time aren't similar structurally (although I haven't 
> exhausted the list yet). I just want to confirm if the folds are truly novel 
> or not.
>
> Thanks in advance for your suggestions,
>
> Nicola

[ccp4bb] 3D Structure Search

[Nicola Evans]

I have recently solved a novel structure which previously did not have any 
structural homologues (as related by sequence identity). I was wondering if 
anyone could recommend a 3D structural search engine? I used the Dali server 
which has been recommended to me in the past (and with past success) but the 
top few hits this time aren't similar structurally (although I haven't 
exhausted the list yet). I just want to confirm if the folds are truly novel or 
not.

Thanks in advance for your suggestions,

Nicola

Re: [ccp4bb] protein quasicrystals?

[Richard Staples]

I agree with Joe CrysAlisPro works very well.



Dr. Richard J. Staples
Crystallographer
Department of Chemistry
578 S. Shaw Lane
Michigan State University
East Lansing, MI 48824
stap...@chemistry.msu.edu
517-353-1074
Lab: 517-353-1079



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joseph 
Ferrara
Sent: Thursday, February 15, 2018 4:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

Nakane-san,

There is also CrysAlisPro, which can handle multiple crystals and may already 
support your detector. If you send me the data, offline, I would be happy to 
pass it onto the CrysAlisPro development team for testing.

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> > on behalf of Yu Qiu
> >
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

Re: [ccp4bb] protein quasicrystals?

[Joseph Ferrara]

Nakane-san,

There is also CrysAlisPro, which can handle multiple crystals and may already 
support your detector. If you send me the data, offline, I would be happy to 
pass it onto the CrysAlisPro development team for testing.

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> > on behalf of Yu Qiu
> >
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>

[ccp4bb] Open-SESAME and Instruct-ERIC workshop: “Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science”, Rehovot, Israel, May-14-18, 2018

[Rikkert Wierenga]

Dear All,



>From May-14 to May-18, 2018 we are organizing an Open-Sesame and Instruct-ERIC 
>workshop: “Remote X-ray data collection from European synchrotrons at the 
>Weizmann Institute of Science”, Rehovot, Israel. The program of this workshop 
>has been updated, please check at 
>http://www.weizmann.ac.il/conferences/RXDC2018/program-outline .



This workshop is organized in the context of the EU projects Open SESAME and 
Instruct-ERIC, together with DLS (Diamond, Oxford, UK), and ESRF (Grenoble, 
France) and the support of FEBS (Federation of European Biochemical Societies). 
The protocols for using ISPyB, remote data collection and data processing at 
DLS and ESRF will be discussed, demonstrated and used. The workshop will 
consist of lectures, tutorials, demonstrations and hands-on remote data 
collection sessions at DLS and ESRF using either test crystals or student 
crystals. Experts are on-site for carrying out the remote data collection 
sessions as well as to demonstrate how to use the pipelines on data processing 
and structure determination calculations available at the ESRF and DLS. 
Additionally, computing facilities and experts are available for on site data 
processing and structure improvement/structure validation calculations. These 
topics will also be introduced by targeted presentations and tutorials as 
outlined in the updated program outline.



The remote data collection at ESRF and DLS is scheduled for the 2nd and 4th day 
of the workshop, respectively. All information on the workshop and on the 
application details are available at 
http://www.weizmann.ac.il/conferences/RXDC2018 . There is no registration fee, 
and the workshop will cover the costs of room & board, at the Weizmann 
Institute, for participants.




Travel fellowships are available, please request such support in the motivation 
letter. The workshop will be limited to a maximum of 25 participants, and the 
deadline for registration is 11.03.2018.



For those unable to make it in person, the meeting will be streamed on the 
internet via Zoom Video Conferencing. Details of the url will be sent out and 
posted on the Conference web site prior to the start of the workshop.



This workshop is particularly targeted for PhD students and postdocs having 
projects aimed at 3D structure determination using biomacromolecular crystals, 
working at institutes that are members of SESAME and/or working at institutes 
of Instruct-ERIC countries relatively far from European Synchrotrons, as well 
as for students from non-EU countries working at EU-institutes who need to 
apply for visa, restricting efficient access to perform on-site data 
collection. Students are encouraged to send crystals in advance, which will 
then subsequently be shipped to DLS or ESRF and used as examples for remote 
data collection.



On behalf of the organizers,



Joel L. Sussman and Rik Wierenga

Website of the workshop: http://www.weizmann.ac.il/conferences/RXDC2018

[ccp4bb] cryoEM cluster

[Raja Dey]

Dear CCP4BB Members,
We like to build our own linux cluster for cryo-EM data analysis. Can
someone suggest a reasonable configuration that we need to buy? Our budget
is about 15K US dollars. Itemize description of what to buy would be very
helpful.
Many thanks for your time and suggestion.
Best regards,
Raja

Raja Dey, Ph. D.
Weill Cornell Medical College,
NY-10065

Re: [ccp4bb] protein quasicrystals?

[Satya]

Hello Yu,

As every one knows, this is major crystallization problem for large
difficult protein targets, specially  proteins with large moving loops
and/or domains may be responsible for this unique crystals/diffraction
pattern. If you think your protein has large moving loop/domain in
presence/absence of ligands, adding specific substrate/additives or
removing loop/domain through site directed mutagenesis or making different
construct of your protein domains (if you are interested in only unique
protein structure)  may be another option to obtained better crystals
depends on the method, which you are going to solve the crystal structure.

This is another way of obtaining better crystals in addition to above
mentioned useful comments.

Wish you good luck for better crystals,
Satya



On Wed, Feb 14, 2018 at 12:33 PM, Kevin Jin  wrote:

> Hi Yu,
>
> I did not see your images before I sent my previous email. I had a same
> case like this long time ago. However, the diffraction image was much worse
> than your. After I modified the condition, I got a single crystal with
> clear edges and reasonable resolution (not diffraction to 2.7 Ang). I have
> no idea which kind of protein you are working on. Membrane protein?
>
> Here is my understanding for your laughing,
>
> 1. According to your diffraction image, those spots (with red circles,
> image attached) may not be diffractions from ice and organic salt. Did you
> use your mouse to check the distance between these spot manually? It may
> give you clues for size of the unit cell, if you can not index it. It will
> be helpful If there was another image with 90 degree offset.
>
> 2. For your first image, folk discussed before here. It is a phase
> separation. In this case, you need to change the ratio between the
> hydrophobic portion (may be a little bit high here?) and hydrophilic
> portion. For instance,
> (1) if you used 20% PEG8K, then you may try 20% PGE 6K or 20% PGE 3300.
> (2) Sometimes, the combination of 2-5% 2-propanol with < 5mM ZnCl2 could
> also give some surprising results.
> (3). Change your salt concentration, and try different anions for
> comparison, Cl vs SO4.
>
> The whole idea above is to fine shuffle the surface charge for better
> packing.
>
> 3. Change your buffer salt with the same pH.
> 4.  You may try some surface detergent.
> 5. Decrease the concentration of your protein sample.
>
> However, each protein has its unique characteristics for crystallization.
>
>  Best Regards,
>
> Kevin
>
> On Tue, Feb 13, 2018 at 1:03 PM, Yu Qiu  wrote:
>
>> As asked by a few people, here are the images of crystals and diffraction.
>>
>>
>>
>> Thanks,
>>
>> Yu
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Keller, Jacob
>> *Sent:* Tuesday, February 13, 2018 4:00 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [EXTERNAL] Re: [ccp4bb] protein quasicrystals?
>>
>>
>>
>> I also would love to see an image….
>>
>>
>>
>> JPK
>>
>>
>>
>> +
>>
>> Jacob Pearson Keller
>>
>> Research Scientist / Looger Lab
>>
>> HHMI Janelia Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>> 
>>
>> Desk: (571)209-4000 x3159 <(571)%20209-4000>
>>
>> Cell: (301)592-7004 <(301)%20592-7004>
>>
>> +
>>
>>
>>
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future.
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>> ] *On Behalf Of *James Phillips
>> *Sent:* Tuesday, February 13, 2018 3:03 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] protein quasicrystals?
>>
>>
>>
>> There are programs which are good at indexing patterns from multiply
>> twinned crystals. Bruker AXS has one, to my knowledge. There may be other
>> sources. I suggest you try that first before you invoke a quasicrystal
>> explanation.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> James Phillips
>>
>>
>>
>> On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane <
>> tnak...@mrc-lmb.cam.ac.uk> wrote:
>>
>> Hi,
>>
>> "dials.reciprocal_space_viewer" is very useful to identify multiple
>> lattices.
>> For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
>> useful.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>
>> > Have you tried microseeding of these sphere crystals? It may help to get
>> > better crystals.
>> >
>> >
>> > Burak
>> >
>> > 
>> > From: CCP4 bulletin board  on behalf of Yu Qiu
>> > 
>> > 

[ccp4bb] PhD Fellowship in cryo-EM at NNF-CPR, University of Copenhagen

[Nicholas Michael I Taylor]

Dear all,

I would like to draw your attention to an open position for a PhD student in my 
group (http://www.cpr.ku.dk/research/protein-structure-function-program/taylor) 
at the Novo Nordisk Foundation Center for Protein Research at the University of 
Copenhagen, where we study the structure of molecular machines by cryo-electron 
microscopy. We have in-house access to a Titan Krios microscope equipped with a 
Falcon 3EC direct electron detector and Volta phase plates.

You can apply for the position (start date: to be discussed but available 
immediately, deadline for application: 28 February 2018) here:

http://employment.ku.dk/phd/?show=146768

Informal enquiries about the position can be addressed to 
nicholas.tay...@cpr.ku.dk.

Best wishes,

Nicholas

Nicholas M. I. Taylor, PhD
Associate Professor

University of Copenhagen
Faculty of Health and Medical Sciences
Novo Nordisk Foundation Center for Protein Research
Blegdamsvej 3B, building 6.1
2200 Copenhagen N
Denmark

TEL +45 35 33 53 37
nicholas.tay...@cpr.ku.dk
http://www.cpr.ku.dk/research/protein-structure-function-program/taylor

[ccp4bb] Two PhD positions in membrane protein structural biology

[Albert Guskov]

Dear all,
I have two openings in my lab to work on:
(1) *TIME-RESOLVED CRYSTALLOGRAPHY*.



This is a collaborative effort of several labs, including experts in
structural biology (Guskov’s lab), biophysics and biochemistry (Slotboom’s
lab), photopharmacology (Szymanski’s lab) and pharmaceutical biotechnology
(Poelarends’ lab). The position is embedded into Guskov’s lab with the
co-supervision from all other PIs.
The general aim of the project is to study dynamic behaviour of amino acid
transporters using novel photocontrolled effectors of amino acid transport
within the context of our photopharmacology program. The specific aim for
this PhD project is (i) to perform thorough biochemical / biophysical
characterization of transport using in-house developed assays, and (ii) to
assist with the structural studies (crystallization, data collection and
refinement).

and 2)

*METAL TRANSPORT**.*
The general aim of this project is to perform structural characterization
of several medically relevant transporters involved in the transport of
metals. This will include biochemical / biophysical characterization and
structural (crystallography and Cryo-EM) investigations.


Since these are the scholarship positions, the whole application process
has to be done via the University's website.


Please apply via

https://www.rug.nl/education/phd-programmes/phd-scholarship-programme/phd-scholarships?details=00347-02S00066GP
(position 1)


or
https://www.rug.nl/education/phd-programmes/phd-scholarship-programme/phd-scholarships?details=00347-02S00066FP
(position 2)


The deadline for applications is the 1st of April, with the envisaged
starting date of the 1st of June


With kind regards,

Dr Albert Guskov,

Assistant Professor / NWO-Vidi fellow,

Biomolecular X-Ray Crystallography,

University of Groningen, the Netherlands