[ccp4bb] map rotation

[Jan Abendroth]

Hi all,
this should be easy, scripting the rotation of a map.
Purpose for this is: Superimpose several structures of the same protein
that crystallized in different space groups, and then drag the maps along.
As a simple test, I took a dimeric protein and try to superimpose molecule
B along with the map on molecule A.

The execution should be straightforward:
a) take a map that covers the unit cell (fft),
b) generate a mask around molecule B (mapmask),
c) apply rotation/translation that I obtain from superimposing molecule B
on molecule A.

The issue is that the obtained map covers both molecule A and B (not a big
deal), more importantly, it cuts of certain areas on both molecules.
Molecule A and B have low RMSDs (0.5Å).

I must be missing something fairly obvious, have not been able to see what.
Feedback would be much appreciated. Scripts are below.

Thanks!
Jan

mapmask \

mapin 2mol_2mFo-DFc.map \

xyzin 2mol_B.pdb \

mskout 2mol_2mFo-DFc_2mol_B.msk \

<< eof

border 2

eof


maprot  \

mapin  2mol_2mFo-DFc.map \

mskin 2mol_2mFo-DFc_2mol_B.msk \

wrkout 2mol_2mFo-DFc_rot.map \

 << eof

MODE from

AVER

ROTA euler  152.440   110.24328.112

TRANS -42.212 5.510   -57.243

eof
-- 
Jan Abendroth
Seattle / Bainbridge Island, WA, USA
home: Jan.Abendroth_at_gmail.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] EMBO Course "Practical Integrative Structural Biology", Nov 3-9 2019, Hamburg

[arjen jakobi]

Posting on behalf of the organiser (Jan Kosinski):

Dear all,

we are happy to announce the upcoming EMBO practical course on “Practical
Integrative Structural Biology” to be held from Nov 3-9, 2019 at EMBL and
the Centre for Structural Systems Biology (CSSB), both on DESY campus in
Hamburg, Germany.

Participants will learn how information from different structural biology
techniques (MX, EM, SAXS and NMR) can be combined with computational
modelling techniques to address the three-dimensional structure of
challenging biomolecular complexes. Participants will collect data at
on-site structural biology facilities, analyse these data and subsequently
build integrative models using major software packages developed by the
invited speakers.

We have put together a diverse and in-depth program of talks and practicals
covering all of the above topics, each of them taught and supervised by
outstanding experts and software developers in their respective fields.

Interested? Then please apply via the course website:
http://meetings.embo.org/event/19-integrative-structural-biology.

On behalf of the organisers,

Jan Kosinski  (organiser)
Matthias Wilmanns (co-organiser)
Arjen Jakobi  (co-organiser)



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Webinar: single particle cryo-electron microscopy in drug discovery

[H. Raaijmakers]

THE EMERGING ROLE OF CRYO-ELECTRON MICROSCOPY IN DRUG DISCOVERY

 This webcast looks at the emerging role of cryo-EM in drug discovery
and its application to resolve the structure of challenging targets,
such as GPCRs. Experts will share their success in cryo-EM enabled
structure-based drug design (e.g. structure-based vaccine design) and
the strength of combining cryo-EM with computational chemistry.

 Speakers:
 Dr. Priyanka Abeyrathne,
 Expert Scientist, Structural Biology & Biophysics,
 Vaccines GlaxoSmithKline

 Dr. Rob Cooke,
 SVP, Head of Biomolecular Structure,
 Sosei Heptares

 March 26, 2019 15:00 GMT

 URL: 
https://cen.acs.org/media/webinar/thermo_032619.html?utm_source=Webinar_medium=Webinar_campaign=CEN

 Cheers,

 Hans Raaijmakers 
Staff scientist Cryo-EM Pharma 
Thermofisher scientific 
hans.raaijmak...@thermofisher.com



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] ABP1 has no known function

[Hughes, Jon]

Dear all,
Many people know much more about the plant hormone auxin than I do, but I 
believe I am right in saying that, despite Romana Gáborová's current PDBe 
highlight on auxin binding protein 1 (ABP1) at 
https://www.ebi.ac.uk/pdbe/about/news/growth, there is currently no valid 
evidence that ABP1 has any physiological function whatsoever (see in particular 
Gao et al. 2015, doi: 10.1073/pnas.1500365112). The structure of the known 
auxin receptor TIR1 (Tan et al. 2007, DOI: 
10.1038/nature05731) is much more 
interesting anyhow!
Best,
jon

--
Professor Jon Hughes, BSc, PhD
Institute for Plant Physiology
Justus Liebig University, Giessen
Zeughaus, Rm. 341
Senckenbergstr. 3
D35390 Giessen, Germany.
work phone: (+49/0)6419935430
fax:  (+49/0)6419935429
mobile:   (+49/0)1757929098
email:  jon.hug...@uni-giessen.de
homepage:
http://www.uni-giessen.de/fbz/fb08/Inst/pflphys
Sent without the use of Apple products





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Deposition requirement of anomalous pairs?

[Randy Read]

I’d be with you, Graeme, as a good compromise between merged data and raw 
diffraction images.  Though it does seem to be getting more practical to make 
image data available…

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 20 Mar 2019, at 12:31, graeme.win...@diamond.ac.uk 
>  wrote:
> 
> Hi Eleanor
> 
> I’d raise you scaled but unmerged intensities :-)
> 
> Best wishes Graeme
> 
> 
> On 20 Mar 2019, at 12:21, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
>  wrote:
> 
> 
> Wouldn't it be a good idea if the pdb required that data deposition provide h 
> k l I+ SIGI+  I- SIGI-  ??
> 
> Even if the depositor has not exploited the anomalous signal, it may well be 
> there sufficiently strongly to validate CYS or phosphates.
> 
> I believe aata processing programs provide this information ?
> 
> Eleanor Dodson
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> -- 
> 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Deposition requirement of anomalous pairs?

[Robbie Joosten]

Hi Eleanor,

That would be a great idea. We would use these data a lot for validation.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Wednesday, March 20, 2019 13:21
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Deposition requirement of anomalous pairs?
> 
> 
> Wouldn't it be a good idea if the pdb required that data deposition provide h
> k l I+ SIGI+  I- SIGI-  ??
> 
> Even if the depositor has not exploited the anomalous signal, it may well be
> there sufficiently strongly to validate CYS or phosphates.
> 
> I believe aata processing programs provide this information ?
> 
> Eleanor Dodson
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Deposition requirement of anomalous pairs?

[graeme.win...@diamond.ac.uk]

Hi Eleanor

I’d raise you scaled but unmerged intensities :-)

Best wishes Graeme


On 20 Mar 2019, at 12:21, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:


Wouldn't it be a good idea if the pdb required that data deposition provide h k 
l I+ SIGI+  I- SIGI-  ??

Even if the depositor has not exploited the anomalous signal, it may well be 
there sufficiently strongly to validate CYS or phosphates.

I believe aata processing programs provide this information ?

Eleanor Dodson



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 
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:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Deposition requirement of anomalous pairs?

[Eleanor Dodson]

Wouldn't it be a good idea if the pdb required that data deposition provide
h k l I+ SIGI+  I- SIGI-  ??

Even if the depositor has not exploited the anomalous signal, it may well
be there sufficiently strongly to validate CYS or phosphates.

I believe aata processing programs provide this information ?

Eleanor Dodson



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Fully funded MSD (Masters by Research) studentships at the University of Essex

[Hough, Mike]

Dear CCP4bbers,

I would be grateful if you could pass details of the below studentships to any 
interested final year undergraduates.

Many thanks,

Mike




Fully Funded Christine Desty MSD positions

These scholarships are for a one year research-based Master’s degree (MSD) that 
have all fees paid and a stipend of ~£15,000. The full list of projects and 
information on how to apply is available here:
https://www.essex.ac.uk/departments/biological-sciences/scholarships-and-funding

https://www.findaphd.com/phds/project/mining-for-novel-cu-proteins-in-ammonia-oxidising-archaea-a-missing-link-in-the-nitrogen-cycle-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107794
This project aims to characterise novel copper enzymes from archaea that may 
represent a missing link in the global nitrogen cycle. The project will 
encompass biochemistry, structural biology and microbiology. Supervised by Dr 
Mike Hough, Dr Corinne Whitby, Dr Richard Strange and Dr Jonathan Worrall.

https://www.findaphd.com/phds/project/creating-the-next-generation-lpmos-for-biofuel-production-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107760
This project will involve the optimisation of an enzyme for the production of 
biofuels - and is directly relevant to industrial biotechnology. Supervised by 
Dr Jonathan Worrall and Dr Mike Hough.

https://www.findaphd.com/phds/project/effect-of-oxidative-stress-on-the-biochemistry-of-dimethylsulfoniopropionate-dmsp-lyase-enzymes-in-tropical-reef-organisms-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107911
In this project you will characterise the role of DMSP lyase enzymes in 
organisms from tropical reefs. Supervised by Dr Michael Steinke, Dr Jonathan 
Worrall and Dr Mike Hough.

https://www.findaphd.com/phds/project/high-throughput-drug-screening-of-a-cancer-target-using-room-temperature-serial-crystallography-to-start-october-2019-for-an-msc-by-dissertation-msd/?p107795
This project will use novel X-ray crystallography methods to screen for the 
binding of drug-like molecules to a cancer target protein. This will involve 
molecular biology, biochemistry and structural biology and is supervised by Dr 
Mike Hough and Dr Filippo Prischi.

The application deadline is Wednesday, April 24.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Java based structural database websites

[John Berrisford]

I can second the recommendation of the Mol* project.

 

Some of the data which is used for Olderado and Vivaldi is now part of the 
wwPDB validation report. 

 

This data is available from the PDBe API

http://www.ebi.ac.uk/pdbe/api/doc/validation.html

 

Additional data NMR validation data is planned to be added to the wwPDB 
validation report later this year. 

 

This data will be displayed in Mol* on PDBe webpages when Mol* is incorporated 
into our web pages. 

 

John

 

From: CCP4 bulletin board  On Behalf Of Jose Duarte
Sent: 19 March 2019 18:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Java based structural database websites

 

Indeed java in the browser was killed a long time ago.

 

But the good news is that plenty of alternatives exist, written in native (to 
the browser) javascript. Wikipedia has a nice compilation of the different 
viewers, under the "Web-based systems" section:

 

https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems

 

I would particularly recommend the Mol* project:

 

https://molstar.org/

 

Jose

 

 

On Tue, 19 Mar 2019 at 10:37, Robbie Joosten mailto:robbie_joos...@hotmail.com> > wrote:

Hi Nick,

 

A bit of a hack I suppose, but you could use a (single use) VM with some old 
windows version that still works. 

E-mailing the developers directly is the way to go to figure out whether you 
can expect an update.

 

We had a similar problem with our own webserver (the Crystallographic Construct 
Designer ccd.rhpc.nki.nl  ) which was completely a java 
applet. The only real solution was a full rewrite. But that requires funding 
which  we luckily got from the West-Life project. 

Keeping websites online is is not easy with changing technology and getting 
funding is hard because it is not new science.

 

Cheers,

Robbie

 

 

 

On 19 Mar 2019 17:43, Nicholas Keep mailto:n.k...@mail.cryst.bbk.ac.uk> > wrote:

This is slightly off topic but I suspect people from PDBe etc read this 
bulletin board. 

Quite a number of very useful structural biology web sites (Olderado, 
Vivaldi, EMDB to name but a few) require java based viewers and hence no 
longer have full (or in the case of vivaldi any) functionality on up to 
date browsers. 

On a new computer it may prove hard or even impossible to find a browser 
that will work 

Are there plans to update these websites and is there any suggeted time 
scale? 

Any work rounds? 

Best wishes 

Nick 

-- 
Prof Nicholas H. Keep 
Executive Dean of School of Science 
Professor of Biomolecular Science 
Crystallography, Institute for Structural and Molecular Biology, 
Department of Biological Sciences 
Birkbeck,  University of London, 
Malet Street, 
Bloomsbury 
LONDON 
WC1E 7HX 

email n.k...@mail.cryst.bbk.ac.uk   
Telephone 020-7631-6852  (Room G54a Office) 
   020-7631-6800  (Department Office) 
Fax   020-7631-6803 
If you want to access me in person you have to come to the crystallography 
entrance 
and ring me or the department office from the internal phone by the door 

 

To unsubscribe from the CCP4BB list, click the following link: 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
 =1 

 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
 =1 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
 =1 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] The PDB Archive Reaches a Significant Milestone - 150,000 entries

[John Berrisford]

With this week's update, the PDB archive has passed the milestone of 150,000
entries, and now contains a total of 150,145.

With this week's regular update, the PDB welcomes 262 new structures into
the archive. These structures join others vital to research and education in
fundamental biology, biomedicine, and bioenergy. Since its inception, the
size of the archive has increased tenfold roughly every 10-15 years: the PDB
reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in
the year 2000. Now that the 150,000th is made available, more than half of
the archive has been released in the past ten years.

The scientific community eagerly awaits the next 150,000 structures and the
invaluable knowledge these new data will bring. However, the increasing
number, size and complexity of biological data being deposited in the PDB
and the emergence of hybrid structure determination methods constitute major
challenges for the management and representation of structural data. wwPDB
will continue to work with the community to meet these challenges and ensure
that the archive maintains the highest possible standards of quality,
integrity, and consistency.

Development and future of the PDB archive and wwPDB organization is
described in the new reference publication for the PDB archive: Protein Data
Bank: the single global archive for 3D macromolecular structure data (
 Nucleic Acids Res., 2019) and many
other papers, including Protein Data Bank (PDB): The Single Global
Macromolecular Structure Archive (
 Methods in Molecular
Biology, 2017), How community has shaped the Protein Data Bank (
 Structure, 2013), and Creating
a Community Resource for Protein Science (
 Protein
Science, 2012).   A full list
is available.

For the full story see the wwPDB news release
 

 

The wwPDB

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Configuration of inositol hexaphosphate

[Robbie Joosten]

Hi Karthik,

There are currently three epimers of inositol hexaphosphate in the PDB: I6P 
(one axial), IHP (the same, which shouldn't be allowed), KGN (two axial, next 
to each other). I could not find other configurations. Which restraint file for 
COOT/CCP4 are you referring to? It might need fixing. 

Cheers,
Robbie 
 


> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Karthik
> Selvam
> Sent: Wednesday, March 20, 2019 11:34
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Configuration of inositol hexaphosphate
> 
> Dear CCP4 community,
> 
> We are working on a complex involving inositol hexaphoshpate. The
> structure of the ligand given in the coot monomer library has alternate
> phosphate groups attached to the ring carbon atoms at the equatorial
> configuration and axial configuration. We also examined the structure of the
> ligand in PDB IDs 2fvv, 2q9p, 1dkp, and 1bq3. They have different
> configurations. All of which are again different from that given in the coot
> library. We shall be grateful if the community could enlighten on this issue.
> 
> Regards,
> Karthik &
> Prateek Raj.
> 
> 
> https://drive.google.com/open?id=13D5j2u_0OxP_X25B_kjKShtV7GQQTwBd
> 
> 
> https://drive.google.com/open?id=1xYc-
> PJ6jBi8UowsYb9MCZ7QEVW6m30KR
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Configuration of inositol hexaphosphate

[Phil Evans]

The stable conformation should be 5 equatorial and one axial (2-position I 
think)

> On 20 Mar 2019, at 10:34, Karthik Selvam  wrote:
> 
> Dear CCP4 community,
> 
> We are working on a complex involving inositol hexaphoshpate. The structure 
> of the ligand given in the coot monomer library has alternate phosphate 
> groups attached to the ring carbon atoms at the equatorial configuration and 
> axial configuration. We also examined the structure of the ligand in PDB IDs 
> 2fvv, 2q9p, 1dkp, and 1bq3. They have different configurations. All of which 
> are again different from that given in the coot library. We shall be grateful 
> if the community could enlighten on this issue.
> 
> Regards,
> Karthik &
> Prateek Raj.
> 
> 
> https://drive.google.com/open?id=13D5j2u_0OxP_X25B_kjKShtV7GQQTwBd
> 
> https://drive.google.com/open?id=1xYc-PJ6jBi8UowsYb9MCZ7QEVW6m30KR
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Configuration of inositol hexaphosphate

[Karthik Selvam]

Dear CCP4 community,

We are working on a complex involving inositol hexaphoshpate. The structure
of the ligand given in the coot monomer library has alternate phosphate
groups attached to the ring carbon atoms at the equatorial configuration
and axial configuration. We also examined the structure of the ligand in
PDB IDs 2fvv, 2q9p, 1dkp, and 1bq3. They have different configurations. All
of which are again different from that given in the coot library. We shall
be grateful if the community could enlighten on this issue.

Regards,
Karthik &
Prateek Raj.


https://drive.google.com/open?id=13D5j2u_0OxP_X25B_kjKShtV7GQQTwBd

https://drive.google.com/open?id=1xYc-PJ6jBi8UowsYb9MCZ7QEVW6m30KR



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1