Re: [ccp4bb] Twin law definition in REFMAC5

[Petrus Zwart]

On Mon, Jul 6, 2020 at 10:33 PM Petr Kolenko 
wrote:

> Dear Eleanor,
> The unit cell parameters are 117.385  155.506  155.611  90.00  90.00
> 90.00, as you expected. The twin law was recognized using phenix.xtriage.
> If I refine the structure using phenix.refine with no twin law and the
> Rwork/free values were 28/33. With the twin law "-h,l,k" the R values are
> 22/28. Moreover, many weird features of the electron density map
> disappeared. But I used phenix.refine only as a proof, because I refined
> the structure using REFMAC5 from the beginning and I do not want to change
> the refinement program during the structure refinement.
>


you break my heart 

:-)




> Thank you for your response,
> Petr
>
> 
> From: Eleanor Dodson 
> Sent: Tuesday, July 7, 2020 7:08:44 AM
> To: Petr Kolenko
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Twin law definition in REFMAC5
>
> Is that twin law possible? Presumably the cell lengths for b and c are
> close but you are swapping a 2fold axis along c for a 21 axis along b?
> Eleanor
>
> On Tue, 7 Jul 2020 at 05:36, Petr Kolenko  > wrote:
> Dear colleagues,
> I have a crystal with space group P21212 and merohedral twinning according
> to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5
> recognizes a different twin law and does not refine the structure properly.
> Is there a way to tell REFMAC5 the proper twin law? I tried to find the
> information in the documentation, but I failed. This is an older project
> running under i, not i2.
> Best regards,
> Petr
>
> 
>
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-- 

P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
CAMERA: http://camera.lbl.gov/
-



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Re: [ccp4bb] Twin law definition in REFMAC5

[Petr Kolenko]

Dear Eleanor,
The unit cell parameters are 117.385  155.506  155.611  90.00  90.00  90.00, as 
you expected. The twin law was recognized using phenix.xtriage. If I refine the 
structure using phenix.refine with no twin law and the Rwork/free values were 
28/33. With the twin law "-h,l,k" the R values are 22/28. Moreover, many weird 
features of the electron density map disappeared. But I used phenix.refine only 
as a proof, because I refined the structure using REFMAC5 from the beginning 
and I do not want to change the refinement program during the structure 
refinement.
Thank you for your response,
Petr


From: Eleanor Dodson 
Sent: Tuesday, July 7, 2020 7:08:44 AM
To: Petr Kolenko
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Twin law definition in REFMAC5

Is that twin law possible? Presumably the cell lengths for b and c are close 
but you are swapping a 2fold axis along c for a 21 axis along b? Eleanor

On Tue, 7 Jul 2020 at 05:36, Petr Kolenko 
mailto:petr.kole...@fjfi.cvut.cz>> wrote:
Dear colleagues,
I have a crystal with space group P21212 and merohedral twinning according to 
"-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a 
different twin law and does not refine the structure properly. Is there a way 
to tell REFMAC5 the proper twin law? I tried to find the information in the 
documentation, but I failed. This is an older project running under i, not i2.
Best regards,
Petr



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Re: [ccp4bb] Twin law definition in REFMAC5

[Eleanor Dodson]

Is that twin law possible? Presumably the cell lengths for b and c are
close but you are swapping a 2fold axis along c for a 21 axis along b?
Eleanor

On Tue, 7 Jul 2020 at 05:36, Petr Kolenko  wrote:

> Dear colleagues,
> I have a crystal with space group P21212 and merohedral twinning according
> to "-h, l, k" twin law. If I click "twin" in the interface, REFMAC5
> recognizes a different twin law and does not refine the structure properly.
> Is there a way to tell REFMAC5 the proper twin law? I tried to find the
> information in the documentation, but I failed. This is an older project
> running under i, not i2.
> Best regards,
> Petr
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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[ccp4bb] Twin law definition in REFMAC5

[Petr Kolenko]

Dear colleagues,
I have a crystal with space group P21212 and merohedral twinning according to 
"-h, l, k" twin law. If I click "twin" in the interface, REFMAC5 recognizes a 
different twin law and does not refine the structure properly. Is there a way 
to tell REFMAC5 the proper twin law? I tried to find the information in the 
documentation, but I failed. This is an older project running under i, not i2.
Best regards,
Petr



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[ccp4bb] Scientific Software Developer position at RCSB PDB, UCSD

[Jose Duarte]

The RCSB PDB is seeking a Scientific Software Developer with skills as a
seasoned, experienced bioinformatics programming professional and a broad
understanding of computational algorithms.

The incumbent will develop, implement, and maintain complex scientific and
web-based software systems for the RCSB Protein Data Bank (PDB;
http://www.rcsb.org) at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively
with other software developers and scientists at the San Diego
Supercomputer Center (SDSC) and the RCSB PDB partner sites to expand
RCSB.org's functionality and reliability as a premier biological data and
information resource. S/he will develop new scalable algorithms for the
mining and analysis of the rapidly growing PDB archive using leading edge
Big Data technologies, design and implement user interfaces for the query,
analysis, reporting, and visualization of 3D structural information and
associated annotations, as well as integrate external database resources
with RCSB PDB to provide a structural view of biology. The incumbent will
help lead the design of databases and data warehouses to store and aid in
the query of data and be actively involved in the software development
process, maintenance and system standards for analysis algorithms, tools,
and infrastructure.

Additionally, the incumbent will serve as an expert on relevant scientific
and technical aspects of the various web, web services, and database
components of the RCSB PDB. S/he will stay abreast of the latest
development in structural and computational biology and new technologies,
apply advanced bioinformatics concepts to design, develop, modify, debug,
and evaluate highly complex software programs and web tools, and translate
scientific problems into scalable and maintainable software solutions that
meet end-user needs. The incumbent will also further science through
Scientific Publications, written in collaboration with our team.

More information and how to apply at: https://www.rcsb.org/pages/jobs

---
Jose Duarte
RCSB Protein Data Bank
San Diego Supercomputing Center
UC San Diego



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Re: [ccp4bb] Protein-DNA covalent bond refinement

[Pavel Afonine]

Hi Cristina,

in Phenix it is:

Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can
define bonds, angles, torsions, planes, etc...

Pavel

On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon  wrote:

> Dear all,
>
> I am writing regarding a problem we are facing with the refinement of a
> structure. We would really appreciate it if anybody could suggest how to
> set up geometrical restraints for a protein-DNA covalent bond in Refmac or
> Phenix?
>
> Thanks in advance,
>
> Best wishes,
>
> Cristina
>
>
> --
> Cristina Machón Sobrado, PhD
> Instituto de Biología Molecular Barcelona-CSIC
> Parc Científic de Barcelona
> c/ Baldiri Reixac 10
> 08028 Barcelona
> Spain
>
> Phone: +34934034957
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
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Re: [ccp4bb] cavities volume calculations

[Joana Pereira]

Hi Nathalie,

I think Caver tools can do that: https://caver.cz/index.php?sid=133 


Best wishes
Joana

> On 6. Jul 2020, at 15:39, Nathalie Colloc'h  wrote:
> 
> Hi everybody,
> 
> I am aware of programs which compute the volume of cavities and pockets.
> 
> However, I am looking for a program which can compute the volume around a 
> given point (given by its coordinates), and return also the information about 
> if it is an open surface pocket or an internal cavity.
> 
> Thanks a lot
> 
> Nathalie
> 
> 
> -- 
> Dr. Nathalie Colloc'h
> équipe CERVOxy
> ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
> Centre Cyceron
> bd Becquerel
> 14074 Caen cedex
> France
> 33.2.31.47.01.32
> coll...@cyceron.fr
> http://www.istct.cyceron.fr/
> 
> 
> 
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[ccp4bb] cavities volume calculations

[Nathalie Colloc'h]

Hi everybody,

I am aware of programs which compute the volume of cavities and pockets.

However, I am looking for a program which can compute the volume around 
a given point (given by its coordinates), and return also the 
information about if it is an open surface pocket or an internal cavity.


Thanks a lot

Nathalie


--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 -  CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
coll...@cyceron.fr
http://www.istct.cyceron.fr/



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Re: [ccp4bb] Accessing full list of programs in CCP4I2

[Christian Roth]

Hi Kelvin,
not quite sure if I understand you correctly,  but if you press the Task
Manager button you get on the right sight a list of topics (import data,
Molecular Replacemnt etc.) each point can be open up like a file tree to
see all programs or pipelines available. You can search with the search
field (Filter) on top for specific program names.
Does that help?

Cheers
Christian

On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin  wrote:

> Hello,
>
>
>
> I am looking for a way to find the list of programs accessible using the
> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert
> back to version 7.0?
>
>
>
> Best regards,
>
>
>
> Kelvin
>
>
>
> --
> Kelvin Lau
>
> https://people.epfl.ch/kelvin.lau
>
>
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch 
> Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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[ccp4bb] Postdoctoral positions in structural biology of fertilization at Karolinska Institutet and Umeå University

[Luca Jovine]

Thanks to a long-term grant from the Knut and Alice Wallenberg foundation, our 
team (http://jovinelab.org) has 
openings for two postdoctoral fellows to study the molecular basis of gamete 
recognition by cryo-electron microscopy and cryo-electron tomography.

Position 1 - Molecular mechanism of egg-sperm interaction at fertilization by 
single-particle cryo-EM
This project will benefit from a close collaboration with Alexey 
Amunts at 
SciLifeLab, as well as easy access to local cryo-EM 
facilities (Stockholm node of the Cryo-EM Swedish National 
Facility and KI 
3D-EM) that together include 3 x Titan Krios 
with K3 detectors, a Talos Arctica with K2 and a Talos L120C with Ceta-D. 
Joining our groups will thus provide a unique opportunity to build upon the 
strengths of two complementary labs and state-of-the-art technology, in order 
to tackle one of the most fundamental questions in biology and understand how 
life begins.
Candidates must hold (or be about to receive) a Ph.D. degree and have 
significant hands-on experience in structural biology. Although proven 
experience in single-particle cryo-EM and knowledge of helical reconstruction 
will constitute an advantage, excellent candidates with experience in X-ray 
crystallography and a strong interest in learning cryo-EM will also be taken 
into consideration. Additionally, previous experience in mammalian cell 
expression as well as purification and biochemical characterization of 
glycoproteins will be considered an asset. At least one first author paper in a 
high-quality international peer-reviewed journal, fluency in English (both 
written and oral), good team spirit and a very strong personal drive to excel 
in science are required.
For more information about this position, please send an e-mail to 
luca.jov...@ki.se and 
amu...@scilifelab.se. To apply, please use the 
following link (deadline 20 September 2020 at 12:00):
https://ki.varbi.com/se/what:job/jobID:339767/type:job/where:4/apply:1

Position 2 - Structural dynamics of the egg coat at fertilization by cryo-ET
The aim of this project will be to shed light on fertilization by using cryo-ET 
to image different stages of interaction between gametes. By imaging 
frozen-hydrated samples, we will focus on resolving the overall architecture of 
the mammalian zona pellucida and related egg coats, as well as investigating 
how changes in the structure of these extracellular matrices contribute to the 
block to polyspermy.
The project will be carried out in close collaboration with Linda 
Sandblad at Umeå 
University  associated with the Umeå Core facility for 
Electron Microscopy 
(UCEM)
 and Molecular Infection Medicine Sweden (MIMS)  The 
position will be located in the Chemical Biological Centre (KBC) building at 
Umeå University, but may 
also require short visits at our KI laboratory.
Available for the project are a TFS Titan Krios instrument with both Falcon 3 
and K2 direct electron detectors, a Scios DualBeam SEM with Aquilos-upgraded 
cryo-FIB and a Leica Thunder fluorescence microscope with cryo-stage, as well 
as full access to all additional instruments and sample preparation equipment 
at both UCEM and Biochemical Imaging Centre Umeå (BICU).
Qualified applicants should have a Ph.D. degree (or be about to receive one), 
at least one first-author publication in a high-quality international 
peer-reviewed journal and documented experience in biochemistry and cryo-EM, 
together with strong computational skills as well as good knowledge of 
developmental biology. Candidates must be able to carry out independent 
scientific research work and to write scientific reports and manuscripts. 
Fluency in written and spoken English is essential. Emphasis will be placed on 
personal suitability, organizational skills and ability to collaborate with 
other members of the lab and the EM facility staff, as well as on genuine 
enthusiasm for the research area and methodology.
For more information about this position, please send an e-mail to 
luca.jov...@ki.se and 
linda.sandb...@umu.se. To apply, please use the 
following link (deadline 19 August 2020):
https://www.umu.se/en/work-with-us/fellowships-and-grants/6-1250-20

Recognition and fusion of the egg and sperm marks the beginning of the life of 
a new individual. Join these projects to shed light on a biological event that 
is not only fundamental from a basic science point of view, but has also m

[ccp4bb] Accessing full list of programs in CCP4I2

[Lau Kelvin]

Hello,

I am looking for a way to find the list of programs accessible using the new 
7.1 CCP4I2 interface? Is this still possible or do I have to revert back to 
version 7.0?

Best regards,

Kelvin

--
Kelvin Lau
https://people.epfl.ch/kelvin.lau

Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 30267
If unreachable: +41 21 69 34494




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[ccp4bb] CryoEM senior scientist position in Sanofi

[Rak, Alexey /FR]

Dear All,
We are looking to add to our Bio Structure and Biophysics department at 
Integrated Drug Discovery scientific platform in Sanofi – a CryoEM expert.
Principal scientist CryoEM position is announced in our team near Paris.

Please apply using the flowing link - CryoEM expert, senior scientist at 
Sanofi
Best regards,
alexey

   Alexey RAK, PhD
Sanofi Scientific Fellow
Head of Bio Structure and Biophysics
Integrated Drug Discovery

Sanofi R&D
13, Quai Jules Guesde - BP 14  Office: +33 (0) 1 58 93 86 93
94403 Vitry sur Seine Cedex Cell:+33 (0) 6 82 61 51 34
FRANCE   
alexey@sanofi.com
[SANOFI_empoweringLife_logo_H-CMJN]
Please consider the environment before printing this email!





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[ccp4bb] Reminder: Call open for BAG beamtime at DESY beamline P11, PETRA III

[Hakanpää , Johanna]

Dear all,

Please note the approaching deadline for submission of Block Allocation Group 
(BAG) proposals for DESY beamline P11 at the PETRA III synchrotron in Hamburg.

Proposals are to be submitted via https://door.desy.de
The deadline for submission is
--
Monday, 13 July 2020 (until midnight local Hamburg time, UTC+2)
--
This call for BAG proposals relates to beamtime to be allocated during 
2021-2022.

Detailed information, preparation guidelines and a template for BAG proposals 
are provided here:
https://photon-science.desy.de/users_area/user_guide/select_the_proposal_type

Beamline P11 is a versatile beamline dedicated to protein crystallography with 
a sample changer in unipuck format.

We offer various focusing modes with beam size from 5 x 10 um (flux 1 × 10^13 
ph/s at 12 keV at the sample position) to 300 x 300 um. Broad energy range from 
5.5 - 28 keV and Pilatus 6M/Eiger2 16M detectors. Fast sample changer cycle (20 
s) with storage capacity for 23 unipucks (368 samples) and remote access.

For further information please see 
http://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction

On behalf of the P11 team,
Johanna


Johanna Hakanpää, PhD

Scientist, Beamline P11 (PETRA III)
Deutsches Elektronen-Synchrotron DESY
Notkestrasse 85
22607 Hamburg
Germany

Phone: +49 40 8998 5756
Email: johanna.hakan...@desy.de



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[ccp4bb] PyMol: Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[David Krause]

Dear List,

I've posted this question to the PyMol mailing list already,
but i was told that the CCP4 list is a little bit more active.

One of our research groups needs a new 3D PyMol setup.
Looking through the wiki 
(https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most 
prominent way to do 3D seemed through Nvidia's 3D Vision,
but since 3D Vision is discontinued, i struggle a bit to find a good and 
future proof 3D solution.


Can you recommend a 3D Setup?
Should we go VR?

We're planning to use the Commercial PyMol version, not the open source one.


--
Mit freundlichen Grüßen / With kind regards

David Krause
IT
Institute of Biochemistry II

Gustav Embden-Zentrum der Biochemie
Goethe University Frankfurt - Medical Faculty

University Hospital - Building 75
Theodor-Stern-Kai 7
60590 Frankfurt am Main
Germany

+49 (0)69 6301 84971 (Phone)
+49 (0)69 6301 84975 (Fax)
kra...@biochem2.uni-frankfurt.de



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[ccp4bb] Research technician position at EMBL Grenoble

[Jose A. marquez]

A Research Technician position is available in the High Throughput 
Crystallization Laboratory at EMBL Grenoble


The HTX lab is one of the largest platforms for automated macromolecular 
crystallization screening in Europe and is offering services through 
Instruct and the EC-funded project iNEXT-Discovery. The Marquez Team has 
developed stream-lined pipelines for fragment screening by X-ray 
crystallography based on the CrystalDirect technology for automated 
crystal harvesting and the CRIMS software. These pipelines are applied 
to study targets of biotechnological and biomedical relevance. The 
successful candidate will contribute towards the operation of the HTX 
facility, the development of innovative methods in protein 
crystallography and will participate in research projects. Under 
specific circumstances candidates with a PhD and publications who wish 
to change their career path can also be considered. See details attached.


Applications should be submitted through the
www.embl.de/jobs/ portal.

Deadline for applications is August 15th.

For questions concerning this position please contact Jose
Marquez (marq...@embl.fr)

Best regards



Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99
https://embl.fr/htxlab/
_




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EMBL Grenoble - Research Technician - GR00147 - VN.pdf
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