Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Lijun Liu]

If data processing to be ok and all possible monoclinic and orthorombic SG gave unreasonable high Rs, maybe good to give a try with p1 space group?  Since the p-lattice indexing gave same a and  b also very close alpha and beta, it could not exclude the possibility of p1 then twinned (also together with ncs and tNCS) to show higher symmetry? Sent from my iPhoneOn Mar 21, 2023, at 1:25 PM, Jessica Bruhn  wrote:Hi Gianluca,Have you checked for diffraction anisotropy problems? It might be worth running it through the STARANISO webserver: https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can make your data look twinned and elliptical truncation can help improve maps. Good luck!Best,JessicaOn Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:Hello, can you give us a screenshot of a diffraction image, with the caveat that they never look all that good with fine-slicing, still it might help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those space groups. Best wishes, Jon Cooper. jon.b.coo...@protonmail.comSent from Proton Mail mobile Original Message On 21 Mar 2023, 16:43, Gianluca Cioci < 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
  

  
  
Dear All,
I have collected a dataset from a small protein diffracting at
  2.7A resolution, here is the space-group determination from XDS: 

 *  44    aP  0.0  66.3   66.3   83.9  90.2 
  90.1  98.7
   *  31    aP  1.2  66.3   66.3   83.9  89.8  90.1 
  81.3
   *  14    mC 1.3  86.4  100.6   83.9  90.0  90.2 
  90.0 
   *  34    mP 2.9  66.3   83.9   66.3  90.2  98.7 
  90.1
   *  13    oC  3.7  86.4  100.6   83.9  90.0  90.2 
  90.0
   *  10    mC 4.9 100.6   86.4   83.9  89.8  90.0 
  90.0
Clearly, something weird is going on... 

The structure can be solved in C2/P21/C2221 with different number
  of molecules in the AU, with Phaser complaining about strong tNCS
  modulation.
However the maps look bad and the structure is impossible to
  refine (Rfact > 0.5) in all the space-groups that I have tried
  so far... 

Thanks in advance for any advice on how to rescue these data !

Cheers,

GIA





--
Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)
http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://www.pict.ipbs.fr/

Tel: +33 (0)5 61 55 97 68
E-mail: ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil
31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr
  



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[ccp4bb] Core Director III Position at Emory University Integrated Electron Microscopy Core (IEMC)

[Liang, Bo]

Dear Colleagues,

The Robert P. Apkarian Integrated Electron Microscopy Core at Emory seeks to 
appoint an enthusiastic, motivated, and experienced cryo-electron microscopist 
at the Core Director III level. The individual will develop and support service 
offerings in traditional electron microscopy (EM), high-resolution 
single-particle cryo-electron microscopy (cryo-EM), and cryo-electron 
tomography (cryo-ET). The Robert P. Apkarian Integrated Electron Microscopy 
Core has EM resources located at two sites on the Emory campus; This position 
will focus on supporting users at both sites. The EM-level instrumentation at 
Emory includes a ThermoFisher Talos Arctica 200 kV FEG-TEM, a JEOL JEM-2200FS 
200 kV FEG-TEM, a ThermoFisher Talos 120 kV TEM, a JEOL JEM-1400 120 kV TEM, a 
Hitachi HT7700 120 kV TEM, and two FEG-SEMs. Additional preparative equipment 
includes two ThermoFisher Vitrobots, a Gatan CP3, several plasma cleaners and 
carbon evaporators, a Baltec HPM-010 high-pressure freezer, a Leica 
cryo-ultramicrotome, and a Leica freeze substitution device. The facility will 
enable researchers from existing investigators at Emory with established 
strengths in cell biology, bacteriology, virology, and structural biology, as 
well as new investigators from across Emory and the Atlanta area. This facility 
is strongly supported by the institutional commitment to advance EM and 
cryo-EM/cryo-ET at Emory University.

A Master's or Ph.D. degree is required with demonstrated experience in all 
aspects of cellular and macromolecular resolution structure determination using 
cryo-EM/cryo-ET, including sample preparation, image acquisition, and data 
processing and analysis. Strong communication, technical, and teaching skills 
are essential for this position. Previous collaborative experience and user 
training in cryo-EM/cryo-ET would be an advantage.

Key responsibilities include, but are not limited to:
1) Provide excellent maintenance and operation of installed equipment to ensure 
high electron microscope performance and generate high-quality cryo-EM/cryo-ET 
data.
2) Establish robust pipelines to support investigators in project development 
and provide outstanding service, including training new users, facilitating 
negative stain and cryo-EM /cryo-ET sample preparation and image acquisition, 
and providing guidance in data processing and analysis.
3) Work closely with the EM core Scientific Directors and Oversight Committee 
to identify future strategic opportunities for infrastructure investment or 
partnership with other research institutions.

If you are interested, please check the full descriptions of this position, and 
apply through the following website:  
https://staff-emory.icims.com/jobs/107567/job (Job Number: 107567). Thank you, 
and we look forward to working with you!

Sincerely,
Bo Liang

---
Bo Liang, PhD
Associate Professor, Department of Biochemistry, Emory University School of 
Medicine
Co-Scientific Director, Robert P. Apkarian Integrated Electron Microscopy Core 
(IEMC), Emory University



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[ccp4bb] Investigator position at the Hauptman-Woodward medical research Institute in Buffalo, New York

[Edward Snell]

Dear CCP4,

An Investigator Position is available.

The Hauptman-Woodward Medical Research Institute (HWI) seeks a scientific 
investigator to join the scientific efforts at the Institute. Applications in 
the broad areas of structural, computational, or molecular biology are 
solicited.  The Institute seeks exceptional candidates who will direct an 
independently funded research program in important areas of human biology, 
health, or disease.  The Institute houses the National Crystallization Center, 
its own Cryo-EM facility, and operates a beamline at the Advanced Photon 
Source. Preference would be given to candidates that could make good use of one 
or more of these facilities. Candidates are expected to have a Ph.D. or 
equivalent in a relevant field and a strong record of scientific productivity 
and demonstrated funding success.

HWI is celebrating 65 years as an independent research institute and expects to 
make several new hires over the next few years.  Located in Buffalo, New York, 
HWI is at the heart of the Buffalo-Niagara Medical Campus and partners with the 
University at Buffalo, Roswell Park Comprehensive Cancer Center, and other 
institutions.  HWI also has a generous intellectual property-sharing policy for 
candidates with entrepreneurial interests. Interested candidates should submit, 
as a single PDF file, a complete curriculum vitae, a statement of research 
accomplishments, an outline of current and future research, and arrange for 
three letters of recommendation to be sent either to Search Committee, 
Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY  14203, or by 
email to opportun...@hwi.buffalo.edu.  The 
search will remain open until filled.

The Hauptman-Woodward Institute is a welcoming environment and an equal 
opportunity employer, extending employment opportunities to qualified 
applicants and employees on a nondiscriminatory basis without regard to race, 
color, sex, creed, age, religion, national origin, marital status, veteran 
status, sexual orientation, genetic predisposition, carrier status, or 
disability that would prevent the performance of the essential requirements of 
the job with or without a reasonable accommodation in compliance with the 
appropriate New York State and Federal laws, or any other legally protected 
characteristics. This policy applies to all conditions and terms of employment.

Buffalo is an extremely affordable city. Applications are currently being 
reviewed and the position is open until filled. Applicants are encouraged to 
follow the application instructions.

Careers information on a number of positions, including a post-doctoral 
opportunity, is available at https://hwi.buffalo.edu/about-us/careers/.

Sincerely,

Eddie Snell


Edward Snell Ph.D.

President and CEO | Hauptman-Woodward Medical Research Institute
Director | NSF BioXFEL Science and Technology Center
Professor, Materials Design and Innovation | University at Buffalo, SUNY
Fellow of the American Crystallographic Association - The Structural Science 
Society

p: +1 716 898 8631 | f: +1 716 898 8660
e: esn...@hwi.buffalo.edu


Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203-1102
hwi.buffalo.edu


[hwi-logo-primary-horizontal]





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[ccp4bb] CBMS Lecture Series - March 22 @13:30 (EST) - Diana Monteiro (HWI)

[Stojanoff, Vivian]

You and your team are invited to join

Diana Monteiro

Hauptman-Woodward Medical Research
NSF BioXFEL Science and Technology Center

March 22, 13:30 EST

Beyond cryo-crystallography: new technologies for serial and time-resolved 
experiments

https://bnl.zoomgov.com/meeting/register/vJItc-qgqTkrEvDDy1Koep3o6jrqajWyhRY


Abstract
The advent of cryocrystallography made determining the high resolution of 
proteins using X-ray diffraction truly possible by reducing radiation damage of 
the samples. It is still the most widely used method, accounting for the vast 
majority of structures currently in the Protein Data Bank. But, with the advent 
of brighter X-ray sources (third and fourth generation synchrotrons and X-ray 
free electron lasers), the number of room temperature (RT), protein structures 
determined by X-ray diffraction is increasing once more. The development of 
technologies towards serial crystallography, including sample preparation, 
delivery, hardware and software advances, make these studies possible. RT 
structures show variations in conformations, highlighting structure-function 
relationships important for basic science and drug discovery. In this talk I 
will give an overview of some of the technologies and techniques we have worked 
on in recent years, including their application towards time-resolved 
experiments.

==
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e nsls.lifescien...@gmail.com
w https://www.bnl.gov/ps/lifesciences/

Address:
Center for Biomolecular Structure
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973

Supporting Grants: CBMS is supported by NIH-NIGMS #P30GM133893, and by the 
DOE-BER #KP1605010. Any work performed at NSLS-II is supported by DOE-BES  
under contract # DE-SC0012704.





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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

cell   66.3   66.3   83.9  90.2  90.1  98.7.  P2 or P21 cell
Cell volume:364551.812

 Data line--- cell 86.4  100.6   83.9  90.0  90.2  90.0. Cell volume double
- C2 or C222 or C2221 cell
Cell volume:729240.938. ie

How many residues in your model?
It is hard to decide much without seeing the data..
Eleanor


On Tue, 21 Mar 2023 at 18:25, Jessica Bruhn  wrote:

> Hi Gianluca,
>
> Have you checked for diffraction anisotropy problems? It might be worth
> running it through the STARANISO webserver:
> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
> make your data look twinned and elliptical truncation can help improve
> maps.
>
> Good luck!
>
> Best,
> Jessica
>
> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, can you give us a screenshot of a diffraction image, with the
>> caveat that they never look all that good with fine-slicing, still it might
>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>> space groups.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>
>>
>>  Original Message 
>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>
>> Dear All,
>>
>> I have collected a dataset from a small protein diffracting at 2.7A
>> resolution, here is the space-group determination from XDS:
>>
>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>
>> Clearly, something weird is going on...
>>
>> The structure can be solved in C2/P21/C2221 with different number of
>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>
>> However the maps look bad and the structure is impossible to refine
>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>
>> Thanks in advance for any advice on how to rescue these data !
>>
>> Cheers,
>>
>> GIA
>>
>>
>> [image: Click to zoom the image]
>>
>>
>> --
>> Dr. Gianluca CIOCI
>> Toulouse Biotechnology Institute 
>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>
>> Tel: +33 (0)5 61 55 97 68
>> E-mail: ci...@insa-toulouse.fr
>>
>> TBI - INSA Toulouse
>> 135 avenue de Rangueil
>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] HTX Center at HWI User Meeting Announcement

[Sarah Bowman]

Hi CCP4BB!

I am excited to announce that the National High-Throughput Crystallization 
(HTX) Center at HWI will be hosting a Virtual User's Meeting!

The meeting is scheduled on Friday 3/31/2023 from 10am-3pm (Eastern).  Register 
here!
Note there is no registration fee for the Virtual User Meeting!

The User Meeting will feature invited speakers Professor Karen Allen (Boston 
University), Professor Krystle McLaughlin (Vassar College), and Professor Erik 
Yukl (New Mexico State University), a panel discussion, and updates about 
operations in the HTX Center.

All are welcome – current users, potential new users, people interested in 
crystallization, and people interested in our operations and pipelines at the 
HTX Center!

Please join us!  If you are interested in attending, register here: 
https://us06web.zoom.us/meeting/register/tZAqdu-sqDgiHNYxxdeZgjuR8hHojzJuvvhp

More details about the schedule will be available soon on our website 
(www.getacrystal.org).

Warmly,
Sarah

Sarah EJ Bowman PhD
Associate Investigator | Hauptman-Woodward Medical Research Institute
Director | National High-Throughput Crystallization Center
Research Associate Professor | Department of Biochemistry | University at 
Buffalo

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203



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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Jessica Bruhn]

Hi Gianluca,

Have you checked for diffraction anisotropy problems? It might be worth
running it through the STARANISO webserver:
https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy can
make your data look twinned and elliptical truncation can help improve
maps.

Good luck!

Best,
Jessica

On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, can you give us a screenshot of a diffraction image, with the
> caveat that they never look all that good with fine-slicing, still it might
> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
> space groups.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 21 Mar 2023, 16:43, Gianluca Cioci <
> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Dear All,
>
> I have collected a dataset from a small protein diffracting at 2.7A
> resolution, here is the space-group determination from XDS:
>
>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>
> Clearly, something weird is going on...
>
> The structure can be solved in C2/P21/C2221 with different number of
> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>
> However the maps look bad and the structure is impossible to refine (Rfact
> > 0.5) in all the space-groups that I have tried so far...
>
> Thanks in advance for any advice on how to rescue these data !
>
> Cheers,
>
> GIA
>
>
> [image: Click to zoom the image]
>
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute 
> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>
> Tel: +33 (0)5 61 55 97 68
> E-mail: ci...@insa-toulouse.fr
>
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Jon Cooper]

Hello, can you give us a screenshot of a diffraction image, with the caveat 
that they never look all that good with fine-slicing, still it might help ;-0 
Also, an idea of the R-merge, R-meas, CC-half in some of those space groups.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 21 Mar 2023, 16:43, Gianluca Cioci wrote:

> Dear All,
>
> I have collected a dataset from a small protein diffracting at 2.7A 
> resolution, here is the space-group determination from XDS:
>
> * 44 aP 0.0 66.3 66.3 83.9 90.2 90.1 98.7
> * 31 aP 1.2 66.3 66.3 83.9 89.8 90.1 81.3
> * 14 mC 1.3 86.4 100.6 83.9 90.0 90.2 90.0
> * 34 mP 2.9 66.3 83.9 66.3 90.2 98.7 90.1
> * 13 oC 3.7 86.4 100.6 83.9 90.0 90.2 90.0
> * 10 mC 4.9 100.6 86.4 83.9 89.8 90.0 90.0
>
> Clearly, something weird is going on...
>
> The structure can be solved in C2/P21/C2221 with different number of 
> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>
> However the maps look bad and the structure is impossible to refine (Rfact > 
> 0.5) in all the space-groups that I have tried so far...
>
> Thanks in advance for any advice on how to rescue these data !
>
> Cheers,
>
> GIA
>
> [Click to zoom the image]
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute (TBI)
> http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulouse
> http://www.pict.ipbs.fr/
> Tel: +33 (0)5 61 55 97 68
> E-mail:
> ci...@insa-toulouse.fr
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04
> http://www.toulouse-biotechnology-institute.fr
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] Postdoctoral Positions available at Yale School of Medicine

[Alon, Assaf]

Dear Colleagues

The Alon lab at Yale Medical School has openings for outstanding recently 
graduated scientists who are excited about our research. We seek individuals 
with a passion for research and a strong background in biochemistry, structural 
(cryo-EM, x-ray), molecular or cell biology

We are focused on gaining mechanistic insights into the activation, signaling, 
and ligand recognition of understudied and interesting membrane receptors for 
sterol signaling molecules

We apply a multidisciplinary approach, combining structural biology, 
biophysics, pharmacology, drug discovery, and cell biology

Visit our lab webpage for details: 
https://www.thealonlab.org

A complete list of Dr. Alon’s publications is available at: 
https://www.ncbi.nlm.nih.gov/myncbi/1R_B6vwLTh1/bibliography/public/

Candidates must have a PhD degree or equivalent in biological sciences with not 
more than 1 year of postdoctoral training. Interested candidates should have 
training and experience in two or more of the following:

Protein purification from E. coli, insect and/or mammalian cells
Structural biology (X-ray or cryoEM)
Biochemical and biophysical techniques
Cell biology and imaging (experience with generating CRISPR KO lines is 
preferred)
Computational techniques related to structure or drug discovery such as 
protein design, MD simulations, and virtual docking

Interested applicants should send a cover letter, CV, a 1-page research 
summary, and contact information for three references to Dr. Assaf Alon 
(assaf.a...@yale.edu)

—Assaf

Assaf Alon, Ph.D.
Assistant Professor
Department of Pharmacology
Yale University School of Medicine
333 Cedar Street
SHM B326A
203-737-6238
www.thealonlab.org




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[ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Gianluca Cioci]

Dear All,

I have collected a dataset from a small protein diffracting at 2.7A 
resolution, here is the space-group determination from XDS:


 *  44    aP  0.0  66.3   66.3   83.9  90.2 90.1  98.7
 *  31    aP  1.2  66.3   66.3   83.9  89.8  90.1 81.3
 *  14    mC 1.3  86.4  100.6   83.9  90.0  90.2 90.0
 *  34    mP 2.9  66.3   83.9   66.3  90.2  98.7 90.1
 *  13    oC  3.7  86.4  100.6   83.9  90.0  90.2 90.0
 *  10    mC 4.9 100.6   86.4   83.9  89.8  90.0 90.0

Clearly, something weird is going on...

The structure can be solved in C2/P21/C2221 with different number of 
molecules in the AU, with Phaser complaining about strong tNCS modulation.


However the maps look bad and the structure is impossible to refine 
(Rfact > 0.5) in all the space-groups that I have tried so far...


Thanks in advance for any advice on how to rescue these data !

Cheers,

GIA


Click to zoom the image


--
Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)
http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://www.pict.ipbs.fr/

Tel: +33 (0)5 61 55 97 68
E-mail:ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil
31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr



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[ccp4bb] Updated pipeline for small molecule data processing at PDBe

[David Armstrong]

**

*We have updated the tools used at PDBe and PDBe-KB for processing small 
molecule ligands and their interactions in the PDB archive. This process 
now identifies larger, linked ligands that are composed of individual 
components covalently linked together, allowing these molecules to be 
identified in a standardised manner for the first time.*


*

The ‘pdbeccdutils’ python library 
(https://github.com/PDBeurope/ccdutils) has been developed for the 
processing of small molecules in the PDB and this update sees a number 
of improvements to the pipeline. This process is used to generate data 
in PDBe’s updated CCD files, including standard 2D and 3D depictions, 
fragment and scaffold identification, external database mapping, and more.



The updates to pdbeccdutils includes the addition of a new module to 
determine ‘bound molecules’, defined as multiple, covalently linked CCD 
ligands into a single, larger molecule. There are also updates to the 
underlying packages, including use of RDKit 2022.09.x for generating 
molecular properties, and use of Gemmi for parsing PDBx/mmCIF format 
files. There is one breaking change, which is the replacement of 
ccd_cif_dict with ccd_cif_block in the updated CCD files.



There have also been updates to PDBe Arpeggio, our version of Arpeggio, 
a python library originally developed by the Blundell group. The PDBe 
Arpeggio python library generates interactions data for proteins and 
ligands in the PDB archive. This update to v1.5 includes improvements in 
identification of different molecule types and updates to underlying 
packages, including Open Babel v3.0.0 and inclusion of Gemmi for parsing 
PDBx/mmCIF files.



For more information about the updates to pdbeccdutils and PDBe 
Arpeggio, view the full news item at 
https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe 




Kind Regards,
David Armstrong

*

--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK



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