[ccp4bb] Ligand superposition!

[Subramanian, Ramaswamy]

Hi All,

I have over 50 pdb files that I have downloaded from PDB that all have the same 
ligand bound.

I wamt to superpose the ligands (and move the protein coordinates using that 
matrix).  The goal is for me to see how difference in ligand environments in 
different complexes.

Is there an easy way to do it?  I am sure it has been done before and I do not 
want to reinvent the wheel.

Thanks.



Rams
subra...@purdue.edu






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[ccp4bb] How to change keyboard shortcuts in Coot

[Gong, Zhen]

Dear all,

Can anyone kindly tell me how to change the keyboard shortcuts settings in 
Coot? My “control + g” did not go to the specified atoms anymore. I might have 
changed the shortcut settings by accident. Thank you very much for your help!

Best,
Zhen



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Re: [ccp4bb] Crystallisation textbook

[Mark J. van Raaij]

Dear All,

The Acta Cryst F special issue is also a very good resource (although I admit 
that I am biased).
Can be read online here:
https://journals.iucr.org/special_issues/2016/crystallization/ 

or ordered as a book from the IUCr here:
https://www.iucr.org/publications/iucr/buy

Best wishes,

Mark J van Raaij (Section Editor of Acta Cryst F)
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> On 14 Jul 2023, at 16:19, Hough, Michael (DLSLtd,RAL,LSCI) 
> <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi all,
>  
> I'd be grateful for any recommendations of a good up-to-date textbook 
> covering macromolecular crystallisation. Currently we are using the excellent 
> book by Terese Bergfors (2009) but would be interested if there is anything 
> more recent with discussion around automation, micro-crystallisation and so on
>  
> Many thanks in advance for your help!
>  
> Kind regards,
>  
> Mike 
>  
> -- 
> 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd. 
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> attachments are free from viruses and we cannot accept liability for any 
> damage which you may sustain as a result of software viruses which may be 
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and 
> Wales with its registered office at Diamond House, Harwell Science and 
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>  
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] Crystallisation textbook

[Briony Yorke]

You can pre-order the new edition of Crystallography made crystal clear!
https://blackwells.co.uk/bookshop/product/Crystallography-Made-Crystal-Clear-by-Arwen-R-Pearson-author-Nicholas-Pearce-author-Jennifer-Wierman-author/9780323910484

I’m definitely going to order a copy  - along with Macromolecular 
Crystallization and Crystal Perfection that John has already recommended.

Briony

From: CCP4 bulletin board  on behalf of Hough, Michael 
(DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk>
Date: Friday, 14 July 2023 at 15:19
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Crystallisation textbook
Hi all,

I'd be grateful for any recommendations of a good up-to-date textbook covering 
macromolecular crystallisation. Currently we are using the excellent book by 
Terese Bergfors (2009) but would be interested if there is anything more recent 
with discussion around automation, micro-crystallisation and so on

Many thanks in advance for your help!

Kind regards,

Mike



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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] O-glycans in coot and phenix/refmac

[Nigel Moriarty]

To the point of refining in Phenix, once you have the glycans in place it
should be automatic except for the first link of the tree. Send me the
model and I can provide the necessary files for refinement.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Fri, Jul 14, 2023 at 2:03 AM Keitaro Yamashita <
kyamash...@mrc-lmb.cam.ac.uk> wrote:

> In the monomer library, pyr-SER and pyr-THR links are defined for the
> O-glycosylation. A monomer should belong to the "pyranose" group in
> the library (or in a user-provided dictionary).
>
> Best regards,
> Keitaro
>
> On Fri, 14 Jul 2023 at 09:22, Jon Agirre
> <17a7df66b7b3-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > To the best of my knowledge, there is no o-glycan equivalent of the Coot
> glyco plugin. We (as in YSBL, York) are working with others to provide
> tools to build all kinds of glycans, but there's nothing you can use at
> this point.
> > I would deal with it like I'd do with other modifications, get monomer,
> make the link, repeat. Links are likely to be part of the CCP4 monomer
> library already. Also, they are likely to be short-ish glycans, so
> hopefully the task won't be too onerous.
> > One issue depending on the resolution is the identification of the
> monosaccharides. But you can have a look at some of the many possibilities
> here:
> https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue
> > It might help to look at other o-glycosylated structures in the PDB. You
> can now do pretty powerful searches on the PDB. Alternatively, I'm sure
> someone in my team could provide a list of all o-glycans Privateer can
> detect in the PDB.
> > Hope this helps,
> > Jon
> >
> >
> > On Fri, 14 Jul 2023 at 09:03, Jonas Emsley <
> 8d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> Dear All
> >>
> >>
> >>
> >> We have a crystal structure with O-glycans for the first time attached
> to a Ser and a Thr sidechain
> >>
> >>
> >>
> >> If anyone can recommend the procedure for adding these in coot and
> refining them in phenix /refmac that would be greatly appreciated
> >>
> >>
> >>
> >> All the best
> >>
> >>
> >>
> >> jonas
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> ##
> >> Dr Jonas Emsley
> >> Professor of Macromolecular Crystallography,
> >> Nottingham Biodiscovery Institute
> >> School of Pharmacy,
> >> University of Nottingham,
> >> University Park,
> >> Nottingham.
> >> NG72RD
> >> Tel: +44 1158467092
> >> Fax: +44 1158468002
> >> email:jonas.ems...@nottingham.ac.uk
> >>
> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
> >>
> >> https://orcid.org/-0002-8949-8030
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> This message and any attachment are intended solely for the addressee
> >> and may contain confidential information. If you have received this
> >> message in error, please contact the sender and delete the email and
> >> attachment.
> >>
> >> Any views or opinions expressed by the author of this email do not
> >> necessarily reflect the views of the University of Nottingham. Email
> >> communications with the University of Nottingham may be monitored
> >> where permitted by law.
> >>
> >>
> >>
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >
> >
> > --
> > Dr Jon Agirre
> > Royal Society University Research Fellow (assistant professor)
> > CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
> > York Structural Biology Laboratory, Department of Chemistry
> > University of York, Heslington, YO10 5DD, York, UK
> >
> > 
> >
> > 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] Crystallisation textbook

[John R Helliwell]

Dear Mike,I offer you this suggestion :-global.oup.comwhich is in the OUP and IUCr Book Series. Greetings,John Emeritus Professor John R Helliwell DScOn 14 Jul 2023, at 15:19, Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote:







Hi all,
 
I'd be grateful for any recommendations of a good up-to-date textbook covering macromolecular crystallisation. Currently we are using the excellent book by Terese Bergfors (2009) but would be interested if there is anything more recent
 with discussion around automation, micro-crystallisation and so on
 
Many thanks in advance for your help!
 
Kind regards,
 
Mike 

 
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[ccp4bb] Postdoctoral Research Associate (Cryo-EM STRUCTURAL BIOLOGY) position in the University of Liverpool, UK. (Job reference 062046)

[Antonyuk, Svetlana]

Dear colleagues,

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 enzyme and 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.

This post is available until 30 September 2026.
Please apply via https://bit.ly/062046

You will have a PhD in Structural Biology.

Any applicants who are still awaiting their PhD to be awarded should be aware 
that if successful, they will be appointed at grade 6, spine point 30.  Upon 
written confirmation that they have been successful in being awarded their PhD, 
they will be moved onto grade 7, spine point 31 (£38,205 - £40,521 pa) from the 
date of their award.

The University has the right to close the vacancy early if it is deemed that 
there have been enough applications received

For informal enquires please e-mail Prof. Samar Hasnain 
(ss...@liverpool.ac.uk) or Dr. Svetlana Antonyuk 
(s.anton...@liverpool.ac.uk)




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Re: [ccp4bb] Crystallisation textbook

[Omid Haji-Ghassemi]

When I first started crystallization made crystal clear (by Gale Rhodes) and 
biomolecular crystallography (by Bernhard Rupp) were my favourites.

I think the former may have a new version coming out soon.

Best,
Omid

On Jul 14, 2023, at 08:20, Hough, Michael (DLSLtd,RAL,LSCI) 
<69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote:


[△EXTERNAL]


Hi all,

I'd be grateful for any recommendations of a good up-to-date textbook covering 
macromolecular crystallisation. Currently we are using the excellent book by 
Terese Bergfors (2009) but would be interested if there is anything more recent 
with discussion around automation, micro-crystallisation and so on

Many thanks in advance for your help!

Kind regards,

Mike



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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
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Re: [ccp4bb] Crystallisation textbook

[Hough, Michael (DLSLtd,RAL,LSCI)]

Of course, having sent this email I found the third edition of the same book 
from 2021.

I would still be grateful for other suggestions though

Mike


rom: CCP4 bulletin board  On Behalf Of Hough, Michael 
(DLSLtd,RAL,LSCI)
Sent: Friday, July 14, 2023 3:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Crystallisation textbook

Hi all,

I'd be grateful for any recommendations of a good up-to-date textbook covering 
macromolecular crystallisation. Currently we are using the excellent book by 
Terese Bergfors (2009) but would be interested if there is anything more recent 
with discussion around automation, micro-crystallisation and so on

Many thanks in advance for your help!

Kind regards,

Mike



--

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retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] Crystallisation textbook

[Hough, Michael (DLSLtd,RAL,LSCI)]

Hi all,

I'd be grateful for any recommendations of a good up-to-date textbook covering 
macromolecular crystallisation. Currently we are using the excellent book by 
Terese Bergfors (2009) but would be interested if there is anything more recent 
with discussion around automation, micro-crystallisation and so on

Many thanks in advance for your help!

Kind regards,

Mike

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] O-glycans in coot and phenix/refmac

[Keitaro Yamashita]

In the monomer library, pyr-SER and pyr-THR links are defined for the
O-glycosylation. A monomer should belong to the "pyranose" group in
the library (or in a user-provided dictionary).

Best regards,
Keitaro

On Fri, 14 Jul 2023 at 09:22, Jon Agirre
<17a7df66b7b3-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> To the best of my knowledge, there is no o-glycan equivalent of the Coot 
> glyco plugin. We (as in YSBL, York) are working with others to provide tools 
> to build all kinds of glycans, but there's nothing you can use at this point.
> I would deal with it like I'd do with other modifications, get monomer, make 
> the link, repeat. Links are likely to be part of the CCP4 monomer library 
> already. Also, they are likely to be short-ish glycans, so hopefully the task 
> won't be too onerous.
> One issue depending on the resolution is the identification of the 
> monosaccharides. But you can have a look at some of the many possibilities 
> here: 
> https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue
> It might help to look at other o-glycosylated structures in the PDB. You can 
> now do pretty powerful searches on the PDB. Alternatively, I'm sure someone 
> in my team could provide a list of all o-glycans Privateer can detect in the 
> PDB.
> Hope this helps,
> Jon
>
>
> On Fri, 14 Jul 2023 at 09:03, Jonas Emsley 
> <8d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Dear All
>>
>>
>>
>> We have a crystal structure with O-glycans for the first time attached to a 
>> Ser and a Thr sidechain
>>
>>
>>
>> If anyone can recommend the procedure for adding these in coot and refining 
>> them in phenix /refmac that would be greatly appreciated
>>
>>
>>
>> All the best
>>
>>
>>
>> jonas
>>
>>
>>
>>
>>
>>
>>
>> ##
>> Dr Jonas Emsley
>> Professor of Macromolecular Crystallography,
>> Nottingham Biodiscovery Institute
>> School of Pharmacy,
>> University of Nottingham,
>> University Park,
>> Nottingham.
>> NG72RD
>> Tel: +44 1158467092
>> Fax: +44 1158468002
>> email:jonas.ems...@nottingham.ac.uk
>> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
>>
>> https://orcid.org/-0002-8949-8030
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please contact the sender and delete the email and
>> attachment.
>>
>> Any views or opinions expressed by the author of this email do not
>> necessarily reflect the views of the University of Nottingham. Email
>> communications with the University of Nottingham may be monitored
>> where permitted by law.
>>
>>
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
> --
> Dr Jon Agirre
> Royal Society University Research Fellow (assistant professor)
> CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
> York Structural Biology Laboratory, Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
>
> 
>
> 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] O-glycans in coot and phenix/refmac

[Paul Emsley]

On 14/07/2023 08:52, Jonas Emsley wrote:


Dear All

We have a crystal structure with O-glycans for the first time attached 
to a Ser and a Thr sidechain


If anyone can recommend the procedure for adding these in coot and 
refining them in phenix /refmac that would be greatly appreciated



Hi Jonas,

I didn't get around to adjusting Coot's carbohydrate to build O-linked 
glycans :-(.


If I wanted to build  one today, I'd have to use cut, paste, superpose, 
copy fragment, merge molecules and change chain-ids. Meh.


Once you have built it however, and used Make Link to add the link to 
the header, the refinement linking should be automatic in Coot (because 
the details of the link are in the CCP4 monomer library).


Regards,

Paul.




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Re: [ccp4bb] O-glycans in coot and phenix/refmac

[Jon Agirre]

To the best of my knowledge, there is no o-glycan equivalent of the Coot
glyco plugin. We (as in YSBL, York) are working with others to provide
tools to build all kinds of glycans, but there's nothing you can use at
this point.
I would deal with it like I'd do with other modifications, get monomer,
make the link, repeat. Links are likely to be part of the CCP4 monomer
library already. Also, they are likely to be short-ish glycans, so
hopefully the task won't be too onerous.
One issue depending on the resolution is the identification of the
monosaccharides. But you can have a look at some of the many possibilities
here:
https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue
It might help to look at other o-glycosylated structures in the PDB. You
can now do pretty powerful searches on the PDB. Alternatively, I'm sure
someone in my team could provide a list of all o-glycans Privateer can
detect in the PDB.
Hope this helps,
Jon


On Fri, 14 Jul 2023 at 09:03, Jonas Emsley <
8d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All
>
>
>
> We have a crystal structure with O-glycans for the first time attached to
> a Ser and a Thr sidechain
>
>
>
> If anyone can recommend the procedure for adding these in coot and
> refining them in phenix /refmac that would be greatly appreciated
>
>
>
> All the best
>
>
>
> jonas
>
>
>
>
>
>
>
> ##
> Dr Jonas Emsley
> Professor of Macromolecular Crystallography,
> Nottingham Biodiscovery Institute
> School of Pharmacy,
> University of Nottingham,
> University Park,
> Nottingham.
> NG72RD
> Tel: +44 1158467092 <+441158467092>
> Fax: +44 1158468002 <+441158468002>
> email:jonas.ems...@nottingham.ac.uk
> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
>
> *https://orcid.org/-0002-8949-8030
> *
>
>
>
>
>
>
>
>
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please contact the sender and delete the email and
> attachment.
>
> Any views or opinions expressed by the author of this email do not
> necessarily reflect the views of the University of Nottingham. Email
> communications with the University of Nottingham may be monitored
> where permitted by law.
>
>
>
>
>
> --
>
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-- 
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK



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[ccp4bb] O-glycans in coot and phenix/refmac

[Jonas Emsley]

Dear All

We have a crystal structure with O-glycans for the first time attached to a Ser 
and a Thr sidechain

If anyone can recommend the procedure for adding these in coot and refining 
them in phenix /refmac that would be greatly appreciated

All the best

jonas



##
Dr Jonas Emsley
Professor of Macromolecular Crystallography,
Nottingham Biodiscovery Institute
School of Pharmacy,
University of Nottingham,
University Park,
Nottingham.
NG72RD
Tel: +44 1158467092
Fax: +44 1158468002
email:jonas.ems...@nottingham.ac.uk
http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
[cid:image001.png@01D9B630.47E7F690]https://orcid.org/-0002-8949-8030








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