Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

[Nicholas Clark]

Hi Marco,

"Superpose" in *Coot* will also take any associated ligands along during
the superposition. You can do this under "Calculate-> SSM Superpose". Be
sure to check "move copy of moving structure". The one that moves will show
as "copy of xxx", with xxx being the name of the one that was moved.

Then, after superposition, you can then change the chain of the extra
protein (i.e., the one that has the DNA you want to put in your structure)
to an unused chain ID and make sure your ligand also is assigned to an
unused chain ID (Edit-> Change Chain IDs). Merge the two separate
structures (Edit->Merge molecules).

Finally, either in a text editor or even Pymol, remove the extraneous
protein and save the new file.

Best,

Nick Clark


On Tue, Feb 27, 2024 at 7:55 PM Marco Bravo  wrote:

> Hello all,
> Does anyone know how to save a superimposed pymol or chimerax session as a
> PDB file in correct format so that I can used it for ccp4 refmac? I am
> trying to superimpose a protein with DNA bound onto the same protein from a
> different species without the DNA. I just want the DNA from the protein-DNA
> complex to be superimposed onto the apo protein structure. I have done the
> superimposition and got rid of the protein from the original protein-DNA
> complex and now have the DNA with the apo protein structure. When I try to
> use this new PDB filer for refmac or even MR I get this error.  Refmac:
> Input coordinate file is not complete. Does anyone know how to properly do
> this ?
>
> Thank you
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

[Rajivgandhi Sundaram]

Hi Marco,
You could use the 'combine' command. You could select two models in
chimeraX and which will write a single pdb file.  Look at the below link.

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html

Best,
Rajiv


On Tue, 27 Feb, 2024, 7:54 pm Marco Bravo,  wrote:

> Hello all,
> Does anyone know how to save a superimposed pymol or chimerax session as a
> PDB file in correct format so that I can used it for ccp4 refmac? I am
> trying to superimpose a protein with DNA bound onto the same protein from a
> different species without the DNA. I just want the DNA from the protein-DNA
> complex to be superimposed onto the apo protein structure. I have done the
> superimposition and got rid of the protein from the original protein-DNA
> complex and now have the DNA with the apo protein structure. When I try to
> use this new PDB filer for refmac or even MR I get this error.  Refmac:
> Input coordinate file is not complete. Does anyone know how to properly do
> this ?
>
> Thank you
>
> 
>
> 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
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] Superimposition save as PDB for ccp4 refmac question

[Marco Bravo]

Hello all,
Does anyone know how to save a superimposed pymol or chimerax session as a PDB 
file in correct format so that I can used it for ccp4 refmac? I am trying to 
superimpose a protein with DNA bound onto the same protein from a different 
species without the DNA. I just want the DNA from the protein-DNA complex to be 
superimposed onto the apo protein structure. I have done the superimposition 
and got rid of the protein from the original protein-DNA complex and now have 
the DNA with the apo protein structure. When I try to use this new PDB filer 
for refmac or even MR I get this error.  Refmac:  Input coordinate file is not 
complete. Does anyone know how to properly do this ? 

Thank you



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Re: [ccp4bb] Combating disinformation in science and other areas

[Navdeep Sidhu]

Dear Daniel,

When board members expressed their opinions on social maladies (e.g. 
real or apparent sexism, anti-migrant bias, etc.) in the sciences in the 
past, that was being (divisively) political too--and thankfully so, I think.


An exhortation to refrain from political issues is, like it or not, 
itself political. Why so? Because it implies an exhortation to be 
complacent with the status quo level of various social maladies in the 
sciences and in the society at large, from which the sciences hardly 
stand isolated. (American historian Howard Zinn put it aptly when he 
said, "You Can't Be Neutral On A Moving Train." There's also a nice book 
of his of the same name, with some alternative views on other issues you 
touch on.)


Best regards,
Navdeep

---
Navdeep Sidhu
Germany
Web: https://scholar.google.de/citations?user=ZqU1AE0J&hl=de
---



On 15.02.24 04:40, Daniel M. Himmel, Ph. D. wrote:

Dear all,


That’s a very nice idea to have an app to combat misinformation that can 
undermine the integrity of science and foster mistrust of scientific 
inquiry.But to launch such an app raises the obvious question:



Who is to be the arbiter of what is true and what is “misinformation”?


The way to uphold the integrity of science is with a free exchange of 
ideas, not an app or document that decides which publication or which 
interpretation of the data is real science and which is misinformation.



Thanks go to Bryan Lepore for pointing out that the work of Herbert 
Marcuse (a strong advocate of a brand of Marxism once popular in 
Germany) led to much violence in the USA.Violent revolutions are how a 
great deal of science has been lost during the last several thousand 
years of human history, which is why we’re first determining atomic and 
near-atomic resolution structures in the 20th and 21st centuries, not 
eons ago.



So, my humble request:Can we stick to crystallography and allied fields 
of structure determination on this e-mail list, and not digress into 
divisive politics, please?



Respectfully submitted,

Daniel




Daniel M. Himmel, Ph. D.

Principal, Himmel Sci Med Com, LLC

E-mail: danielmhim...@gmail.com 

URL   : https://himmelscimedcom.com 




On Wed, Feb 14, 2024 at 7:52 AM Bryan Lepore > wrote:


The idea of "Global Sustainability" can be found in the documents
for the noted projects, so the United Nations "Sustainable
Development Goals" appear to be worth reviewing as background - even
though it appears the UN or UNESCO (below) is irrelevant to them :

“Transformation is the red thread running through all the
Sustainable Development Goals, the United Nations’ agenda for
responding to global challenges facing humanity and the planet.
Setting our world on a more sustainable course requires radical
shifts in current development paradigms that are exacerbating
inequalities and imperilling [sic] our common future. This
transition is dependent on new knowledge, research and competences
that only higher education institutions are in a position to
provide, rooted in their historic role of service to society.”

[...]

“In 1964, inspiring the 1968-student revolt a couple of years later,
Herbert Marcuse wrote a key text against “one dimensional man”,
urging universities and campuses around the world to become places
that resisted reductionism. ”


Source:


Parr, et. al.


“Knowledge-driven actions: transforming higher education for global
sustainability”


2022
UNESCO
https://doi.org/10.54675/YBTV1653 




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[ccp4bb] PDRA position in structural biology at Diamond Light Source, 3 year fixed term

[Flaig, Ralf (DLSLtd,RAL,LSCI)]

We now have an opportunity for an experienced molecular structural biologist, 
at Post-Doctoral Research Associate level, to further support the structural 
biology activity
on the I04 beamline in the field of chromatin remodelling and histone 
modification.
These projects are pursued as part of the Diamond inhouse research programme 
and in collaboration with university partners.

Suitable candidates will hold an appropriate first degree and PhD and 
demonstrate proven relevant experience. We are looking for an experienced
molecular biologist or biochemist with experience or a strong interest in 
structural biology and biophysical methods. Experience in a
structural biology method (X-ray crystallography, cryo-EM, SAXS) would be 
highly beneficial, and a keen interest in pursuing an integrated structural 
biology approach is expected.

The candidate will join the team at the Diamond variable and microfocus 
macromolecular crystallography beamline I04 
(https://www.diamond.ac.uk/Instruments/Mx/I04.html) ,
which is part of the MX Group at Diamond and offers capabilities for tackling 
challenging problems in structural biology. The MX group at Diamond presents
7 world-leading MX beamlines with unique capabilities and is complemented by 
dedicated beamlines for bioSAXS, CD, X-ray imaging and spectroscopy,
IR-microspectroscopy, 3D Correlative Cryo-Imaging and the electron Bio-Imaging 
Centre (eBIC). In addition, the MX group has established the first dedicated
X-ray fragment screening lab (XChem) and an XFEL hub which hosts users, and 
coordinates XFEL experiments. There is a strong software development
programme that includes lead development of the DIALS integration software 
package, ISPyB/Synchweb and automation pipelines as well as
collaborative projects with CCP4 and CCP-EM. This is complemented by provision 
of state-of-the-art laboratories for structural biology within
the Research Complex at Harwell. Together with other world leading facilities 
(ISIS, CLF) on the campus and the Rosalind Franklin Institute (RFI)
the Harwell Science and Innovation Campus site offers a stimulating and highly 
multidisciplinary environment.

More details and how to apply can be found here:

https://vacancies.diamond.ac.uk/vacancy/postdoctoral-research-associate-structural-biology-502687.html

Closing date for applications is 10/03/2024.


--
Dr. Ralf Flaig
ralf.fl...@diamond.ac.uk
Principal Beamline Scientist, I04 Macromolecular Crystallography
Diamond Light Source, Harwell Science and Innovation Campus
Chilton, Didcot OX11 0DE, United Kingdom
tel: +44 (0)1235 77 8412 fax: +44 (0)1235 77 8448
http://www.diamond.ac.uk/mx-home/
https://www.diamond.ac.uk/Instruments/Mx/I04.html


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Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] PDRA position in the University of Liverpool (UK)

[Antonyuk, Svetlana]

UNIVERSITY OF LIVERPOOL
DEPARTMENT OF BIOCHEMISTRY AND SYSTEMS BIOLOGY
Cryo-EM STRUCTURAL BIOLOGY POSTDOCTORAL RESEARCH ASSOCIATE


Grade 7 (Salary range £38,250 - £40,521 pa)

An exciting opportunity has emerged to join the Molecular Biophysics 
Group to work on a BBSRC-supported 
collaborative project between the teams from University of Leeds and Liverpool 
aimed at answering fundamental questions on enzyme mechanism of quinol- 
dependent integral membrane nitric oxide reductases, a member of respiratory 
heme- copper oxidase superfamily. The project builds on our recent 2.2Å cryoEM 
structure of this enzymeand aims to address a number of ambitious questions 
through well-informed point mutations and high resolution cryoEM structures. In 
addition to the isolated enzyme, we also aim to obtain the first structures of 
CuNiR-qNOR protein-protein complexes in catalytic turnover.

We require an experienced PDRA with fluency in several elements of a structural 
biology project including cryoEM data collection and processing, model building 
and structure refinement at high resolutions. Experience with protein 
expression and purification of membrane proteins is desirable. The PDRA will be 
assisted by a full-time research associate/research technician for producing 
wild-type and mutant qNOR membrane bound proteins in sufficient quantities for 
functional and cryoEM studies. The RA would also support in producing CuNIRs 
and its mutants following the established protocols in our laboratories.

You should also be able to work in a team and previous experience of working at 
multiple sites would be an advantage. The PDRA is expected to spend significant 
time (typically one week per month) at Leeds where you would be fully 
integrated into Muench’s group. Excellent verbal and written communication 
skills are essential. Closing date for application is 30th March 2024. The post 
is available for immediate start for nearly 3 years.



Please send your CV and cover letter to Professor Samar Hasnain 
(s.s.hasn...@liverpool.ac.uk), Dr Stephen 
Muench (s.p.mue...@leeds.ac.uk) and Dr Svetlana 
Antonyuk (s.anton...@liverpool.ac.uk)



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[ccp4bb] Bursary Extension - Monday 4 March 10th CCP-EM Spring Symposium/DLS BCI User Meeting 30th April - 2nd May 2024

[Tom Burnley - STFC UKRI]

Dear all,

** We have additional bursary places and have extended the bursary deadline to 
Monday 4th March **

This is thanks to kind support from: CryoCloud, CryoSol, Dectris, Quantum 
Detectors, Nanosoft, SubAngstrom and Thermo Fisher Scientific.

The bursaries will cover registration fee and two nights accommodation. If you 
are interested please send a 300 word application to ccpemeve...@stfc.ac.uk 
detailing your interest in attending the conference in person, why this can't 
be covered by other funds and how this would benefit you and others.  We will 
confirm all bursary places by 7th March.

** Early bird registration will now close Monday 11th March **

Confirmed symposium speakers:
Yifan Cheng (UCSF)
Wah Chiu (Stanford)
Hans Elmlund (NIH)
Judy Hirst (MRC-MBU)
Oleg Kovalevskiy (DeepMind)
Martin Pilhofer (ETH Zürich)
Lorenz Lamm (Helmholtz Zentrum München)
Kyle Morris (EBI)
Thomas Mulvaney (CSSB)
David Owen (DLS)
Alexis Rohou (Genentech)
Chris Russo (MRC-LMB)
Carsten Sachse (Jülich)
Helen Saibil (Birkbeck)
Filo Sanchez Rodriguez (York)
Sjors Scheres (MRC-LMB)
Sriram Subramaniam (British Columbia)
Rebecca Thompson (TFS)
Peiyi Wang (SUSTech)
Martyn Winn (STFC)
Tzviya Zeev-Ben-Mordehai (Utrecht)
Xiaodong Zhang (Francis Crick Institute)
Ellen Zhong (Princeton)

Confirmed BCI speakers:
Vicki Gold (Exeter)
Mangala Srinivas (Wageningen)
Stefan Raunser (Max Planck Molecular Physiology)
Plus eBIC user meeting round-table discussion

Symposium scientific organisers:
Peijun Zhang (DLS/Oxford)
Peter Rosenthal (Francis Crick Institute)

Biological Cryo-Imaging user meeting organising committee:
Lorna Malone (eBIC, Diamond)
Archana Jadhav (B24, Diamond)

30th April - 2nd May 2024, EMCC, Nottingham, UK

Full details and schedule:
https://www.ccpem.ac.uk/training/spring_symposium_2024/spring_symposium_2024.php

Registration:
https://cvent.me/Q1QANv

We look forward to welcoming you all in Nottingham!

Best wishes from CCP-EM & DLS BCI



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[ccp4bb] FAPESP Postdoctoral Position on in situ Cryo-Electron Tomography

[Andre LB Ambrosio]

Dear Colleagues,

With the Aquilos 2 cryo-FIB soon available at our Institute (link 1
),
allow me to advertise a fellowship opportunity in my lab briefly:

*Overview*:
This project to be developed at the São Carlos Institute of Physics (IFSC),
University of São Paulo (USP) in Brazil, aims to study the in situ
structure of mitochondrial filamentous enzymes involved in the metabolic
adaptation of tumors and their effects on organelle ultrastructure and
morphology upon filamentation. This research will be an extension of
Adamoski et al., NSMB 2024 (doi: 10.1038/s41594-023-01118-0
), focusing on more profound
questions with cutting-edge methodologies, such as correlative
light-electron microscopy (CLEM), cryo-electron tomography in lamella
(cryo-ET) and expansion microscopy (ExM), that can also be applied to other
proteins in the lab.

*Methodological Responsibilities*:
1) Sample Preparation: Engage in cell culturing, vitrification, and
lamellae preparation in our lab at the IFSC/USP;
2) Data Collection and Processing: Perform high-resolution tomographic data
collection using top-tier microscopy facilities in Brazil and
internationally. Data processing will be done in-house.

*Requirements*:
1) PhD in Chemistry, Biochemistry, Molecular Biology, or related;
2) Experience in Cell Biology; proficiency in cryo-FIB and cryo-ET, or
single-particle cryo-EM is a big plus;
3) Strong analytical, collaboration, and English language skills.

*Details and how to apply*: link 2


This opportunity is open to candidates of any nationality. The selected
candidate will receive a Postdoctoral fellowship from the São Paulo
Research Foundation (FAPESP) for *R$ 9,047.40 monthly* and a research
contingency fund, equivalent to 10% of the annual value of the fellowship,
allocated for research-related expenses.

*Ref: FAPESP Fellowship Opportunity 6788 (POR/EN)*: link 3


Thank you, and enjoy your week.

-- 
Andre LB Ambrosio
Associate Professor, IFSC/USP - Brazil
www.ifsc.usp.br/alba



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