Re: [ccp4bb] Regarding symmetry notion in coot

[Edward A. Berry]

On 06/21/2018 03:34 PM, John Berrisford wrote:

 From a PDB deposition point of view, I echo Paul’s comment. If possible, 
please move your molecule closer to the origin. It helps with the curation 
process and is easier for users of your entry as some software struggles with 
such extreme transformations.

Regards

John


Now that we've all read the manual :),
Since the origin shift in question here is always integral: { 1 0 1 }
It seems this is not about _where_ in the unit cell, but in _which_ unit cell.

As I understand it the symop: -X, Y+1/2, Z + (0 -1 1)
is what would work if you were in the first cell { 0 0 0 }
So you need to
Take the current coordinate X =x,y,z
subtract the origin translation O = { 1 0 1 },
apply the symop S = -X, Y+1/2, Z + (0 -1 1) = -X,Y,Z +(0,-1/2,1)
add back the origin translation O

something like X' = S(X-O) + O

which could take three runs of pdbset.

But you could really work out an operator that would do it in one run:
the symop S consists of a rotation and translation

S(x) = M(x) + T
S(X-O) = M(X-O) +T
S(X-O) = M(X) - M(O) +T
X' = S(X-O) + O = M(X) - M(O) + T + O

In the example given, M = -X,Y,Z; T = (0,-1/2,1); O = (1 0 1)
M(O) = -1,0,1
-M(O) = 1,0,-1
add T gives 1,-1/2,0
add O gives 2,-1/2,1
so the operator should be
-X+2,Y-1/2,Z+1
or something like that, which you could use in pdbset.
Matrix inverts along x, coordinates are way positive in x, result way negative,
  need to add 2 unit cell translations to position it adjacent to orig 
coordinates

Would something like that work?


*From:*CCP4 bulletin board  *On Behalf Of *Paul Emsley
*Sent:* 21 June 2018 17:30
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Regarding symmetry notion in coot

On 20/06/18 20:49, Anurag Misra wrote:

What is the meaning of the last field — the one in curly brackets -- that

describes the symmetry transformation of a given molecule in coot?


See Section 4.11 of Coot User Manual: "Symmetry"


For example, for

a given X Y Z, coot displays the symmetry transformation of an equivalent

position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.

Can the symmetry molecule be written like bellow by summing respective 
values?


In the general case, no. Move your molecule closer to the origin - so that the 
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.

Regards,

Paul.

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Re: [ccp4bb] Regarding symmetry notion in coot

[Eleanor Dodson]

And so does MOLREP..
Phaser too please?

E

And Paul - yes; please cut and paste..
E

On 21 June 2018 at 20:00, George Sheldrick 
wrote:

> For small molecules, programs such as SHELXT move the structure to be as
> near as possible to the center of the unit-cell, not the origin. Failure to
> do so may cause a 'checkCIF alert'.
>
> George
>
>
> On 06/21/2018 09:34 PM, John Berrisford wrote:
>
> From a PDB deposition point of view, I echo Paul’s comment. If possible,
> please move your molecule closer to the origin. It helps with the curation
> process and is easier for users of your entry as some software struggles
> with such extreme transformations.
>
>
>
> Regards
>
>
>
> John
>
>
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel: +49-551-39-33021 or +49-5594-227312
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Regarding symmetry notion in coot

[George Sheldrick]

For small molecules, programs such as SHELXT move the structure to be as 
near as possible to the center of the unit-cell, not the origin. Failure 
to do so may cause a 'checkCIF alert'.


George


On 06/21/2018 09:34 PM, John Berrisford wrote:


From a PDB deposition point of view, I echo Paul’s comment. If 
possible, please move your molecule closer to the origin. It helps 
with the curation process and is easier for users of your entry as 
some software struggles with such extreme transformations.


Regards

John


--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel: +49-551-39-33021 or +49-5594-227312





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Re: [ccp4bb] Regarding symmetry notion in coot

[John Berrisford]

>From a PDB deposition point of view, I echo Paul’s comment. If possible, 
>please move your molecule closer to the origin. It helps with the curation 
>process and is easier for users of your entry as some software struggles with 
>such extreme transformations. 

 

Regards

 

John 

 

From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 21 June 2018 17:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding symmetry notion in coot

 

 

On 20/06/18 20:49, Anurag Misra wrote:

 
What is the meaning of the last field — the one in curly brackets -- that 
describes the symmetry transformation of a given molecule in coot?


See Section 4.11 of Coot User Manual: "Symmetry"




 For example, for 
a given X Y Z, coot displays the symmetry transformation of an equivalent 
position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
 
Can the symmetry molecule be written like bellow by summing respective values?
 

 


In the general case, no. Move your molecule closer to the origin - so that the 
pre-translation is (0,0,0) - then coot will report "conventional" symmetry.

Regards,

Paul.

 

  _  

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Re: [ccp4bb] Regarding symmetry notion in coot

[Paul Emsley]

On 21/06/18 18:36, Eleanor Dodson wrote:
> Paul - where and what is the definition of this line??
>
>

Dear Eleanor,

It is not clear to me how I should answer other than cutting and pasting
Section 4.11 "Symmetry" of the manual. Is that what you want me to do?

Regards,

Paul.



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Re: [ccp4bb] Regarding symmetry notion in coot

[Eleanor Dodson]

Paul - where and what is the definition of this line??

eleanor

On 21 June 2018 at 17:29, Paul Emsley  wrote:

>
> On 20/06/18 20:49, Anurag Misra wrote:
>
> What is the meaning of the last field — the one in curly brackets -- that
> describes the symmetry transformation of a given molecule in coot?
>
>
> See Section 4.11 of Coot User Manual: "Symmetry"
>
>  For example, for
> a given X Y Z, coot displays the symmetry transformation of an equivalent
> position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
>
> Can the symmetry molecule be written like bellow by summing respective values?
>
>
>
>
> In the general case, no. Move your molecule closer to the origin - so that
> the pre-translation is (0,0,0) - then coot will report "conventional"
> symmetry.
>
> Regards,
>
> Paul.
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Regarding symmetry notion in coot

[Paul Emsley]

On 20/06/18 20:49, Anurag Misra wrote:
> What is the meaning of the last field — the one in curly brackets -- that 
> describes the symmetry transformation of a given molecule in coot?

See Section 4.11 of Coot User Manual: "Symmetry"

>  For example, for 
> a given X Y Z, coot displays the symmetry transformation of an equivalent 
> position as " -X, Y+1/2, Z + (0 -1 1) & { 1 0 1 }”.
>
> Can the symmetry molecule be written like bellow by summing respective values?
>
>

In the general case, no. Move your molecule closer to the origin - so
that the pre-translation is (0,0,0) - then coot will report
"conventional" symmetry.

Regards,

Paul.




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[ccp4bb] Director of Institute for Structural and Molecular Biology at UCL/Birkbeck

[Nicholas Keep]

We are looking to recruit a world leading scientist to succeed Prof 
Gabriel Waksman FRS FMedSci as Director of the Institute of Structural 
and Molecular Biology at UCL and Birkbeck, University of London.


The Institute of Structural and Molecular Biology (ISMB) is a 
world-leading interdisciplinary institute in the field of structural, 
molecular and mechanistic biology, and an important strategic 
collaboration between UCL and Birkbeck, University of London. Research 
interests cover a broad range of key research questions in fundamental 
biology, with a particular focus on the mechanisms of molecular 
machines. Our approaches are at the cutting edge of interdisciplinary 
biomolecular science. World-class research facilities are accessible to 
all ISMB members, including laboratories for cryo-electron microscopy, 
X-ray crystallography, NMR spectroscopy, biophysical methods, mass 
spectrometry, computational biology, cell biology, optical microscopy 
and microbiology. ISMB seminars, symposia and retreats facilitate 
collaborative research activities, while our PhD programmes, including 
an ISMB Wellcome Trust funded programme, support recruitment of 
high-calibre students committed to interdisciplinary research.  The 
successful candidate will have a world-class record of research in a 
complementary area, a shared commitment to multidisciplinary and 
multiscalar approaches to mechanistic biology, and a vision to lead the 
ISMB to the next stage of its development.


Details and the application form can be found at
https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTczNDQwNCZ2dF90ZW1wbGF0ZT05NjUmb3duZXI9NTA0MTE3OCZvd25lcnR5cGU9ZmFpciZicmFuZF9pZD0wJnBvc3RpbmdfY29kZT0yMjQ=

For informal enquiries, please contact Professor Frances Brodsky 
(Director, UCL Biosciences and Chair of the Search Committee 
(f.brod...@ucl.ac.uk ) or, for enquiries 
about Birkbeck, Professor Nicholas Keep (n.k...@bbk.ac.uk 
).


Closing Date 31st July 2018



--
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

emailn.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




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[ccp4bb] Postdoctoral Position in Structural and Functional Studies of Telomeric Complexes

[Emmanuel Skordalakes]

A postdoctoral fellow position is immediately available in the laboratory of 
Emmanuel Skordalakes at The Wistar Institute. The laboratory studies protein, 
nucleic acid assemblies that participate in the replication and maintenance of 
telomeres and have been implicated in a host of diseases including cancer. 
Areas of interest include the telomere replication and maintenance 
nucleoprotein complexes telomerase, CST and shelterin. We use a 
multidisciplinary approach involving biochemical, biophysical and cell based 
assays to address mechanistic questions related to the function of the above 
protein-nucleic acid assemblies. Our goal is to understand how telomeres are 
replicated, how shelterin and CST regulate this process and how dysfunction of 
these complexes leads to human disease. Information obtained from these studies 
will be used to identify activity modulators of telomerase and associated 
complexes as potential therapeutics for cancer and age-related diseases.
The laboratory is located in the University City area of Philadelphia, in the 
heart of the University of Pennsylvania Campus. Both the Wistar Institute and 
the University of Pennsylvania provide resources to conduct cutting edge 
collaborative research, outstanding intellectual environments and 
state-of-the-art facilities.
We are looking for highly motivated candidates that have recently acquired or 
will be acquiring a Ph.D. in biochemistry, structural biology or a related 
field and have a record of peer reviewed publications. Additional information 
regarding our research program can be found at the laboratory's web sites
http://webdev.chem.upenn.edu/chem/research/faculty.php?id=52
http://www.wistar.org/lab/emmanuel-skordalakes-phd
Interested applicants should e-mail their CV along with a cover letter briefly 
describing their research accomplishments and current research interests to 
Emmanuel Skordalakes, Ph.D., Associate Professor 
(sko...@wistar.org).
Emmanuel Skordalakes, Ph.D.
Associate Professor
Gene Expression and Regulation Program

The Wistar Institute
3601 Spruce St
Philadelphia, PA 19104
215-495-6884 Office
215-898-2202 Lab
sko...@wistar.org






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[ccp4bb] Postdoctoral Position in Structural Biology at Upstate Medical University - Syracuse, NY

[Dipak Patil]

*On behalf of Prof. Richard JH Wojcikiewicz*



A post-doctoral position is available immediately for a highly-motivated
individual to perform NIH-funded work on the structure and function of the
erlin1/2 complex; see Wright and Wojcikiewicz (2016) Prog. Mol. Biol.
Trans. Sci. 141, 141-159; Pearce at al. (2009) J. Biol. Chem. 284,
10433-10445. Primary goals will be to express and solve the structure of
the erlin proteins, to utilize cryo-EM to generate a high-resolution
structure of the erlin1/2 complex and use CRISPR/Cas 9-based approaches to
define the interface between activated IP3 receptors and the erlin1/2
complex. The successful candidate will join a highly active lab focused on
signaling via IP3 receptors in mammalian cells. Applicants must have a
Ph.D. degree in biological sciences with strengths in structural biology,
biochemistry and cell biology. The candidate is expected to drive forward
the project, act semi-independently, compile and analyze and write up data
for publication, and work co-operatively with others.



For consideration, please send your CV, three references and other relevant
information to Professor Wojcikiewicz at the site:



https://jobsatupstate.peopleadmin.com/applicants/Central?quickFind=215257


Thanks,
Dipak

-- 

Dr. Dipak N. Patil

Department of Neuroscience

The Scripps Research Institute

130 Scripps Way, 3C2

Jupiter, Florida 33458



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[ccp4bb] Software Engineer position to work with Phaser team in Cambridge

[Randy Read]

We've just advertised a position for a Software Engineer to work with us on the 
development of Phaser.  Detailed information on the position and how to apply 
can be found on the University of Cambridge website 
(http://www.jobs.cam.ac.uk/job/17918/) and on jobs.ac.uk 
(http://www.jobs.ac.uk/job/BKS034/software-engineer).

The text of the job description is appended, if you'd like to look at that 
before clicking on one of the links!

Best wishes,

Randy Read

=

We are looking for a graduate Software Engineer to join the group of Prof Read 
in the Cambridge Institute for Medical Research (http://www.cimr.cam.ac.uk/), 
based at the Cambridge Biomedical Campus in Cambridge. The well-established 
project develops mathematical methods and software for the imaging of 
biological molecules. The software supports academic and pharmaceutical R&D 
worldwide.

You will be joining a small expert academic team. The successful applicant will 
have a careful approach to software development. Your software will be required 
to be reliable, algorithmically fast, and memory efficient. We have a slow 
development cycle and the code you write will be in use for the foreseeable 
future. Your individual contribution will be recognised with authorship of 
peer-reviewed articles; publications from our group have a track record of 
being highly cited.

The project is funded by the National Institute of Health (USA) and the 
successful applicant will have the opportunity to join bi-annual collaborative 
meetings that cycle among Lawrence Berkeley National Laboratory (Berkeley, 
California), Duke University (Durham, North Carolina) and the New Mexico 
Consortium (Santa Fe, New Mexico). We also have an active collaboration with 
IBMB- CSIC (Barcelona, Spain).

Software is open source 
(https://git.uis.cam.ac.uk/x/cimr-phaser/phaser.git/summary). We use the 
C++0x/C++11 standard to maintain cross-platform compilation and compatibility. 
You will have access to the University of Cambridge's computing resources, and 
a laptop will be provided.

Qualifications and Experience: University degree that includes computer science 
and/or mathematics, experience with C++ and the Linux OS. Skills in Python 
scripting, GPU programming and threading would be desirable. Knowledge of 
biology to A level standard or equivalent would be an advantage.

This appointment is full-time (37 hours/week Monday to Friday) but we welcome 
applications from individuals who wish to be considered for part-time working 
or other flexible working arrangements.

Royalty payments from software will extend beyond the lifetime of the contract. 
University of Cambridge employment benefits include USS pension, and reduced 
staff fees for University of Cambridge graduate courses (see 
http://www.jobs.cam.ac.uk/offer/ for a full list).

For more information on the research group see 
https://www.cimr.cam.ac.uk/research/principal-investigators/principal-investigators-q-z/read,
 and details of the Phaser project can be found at 
http://www.phaser.cimr.cam.ac.uk/.

Fixed-term: The funds for this post are available untill 30th April 2022.
--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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



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[ccp4bb] Postdoc in enzyme dynamics

[Magnus Wolf-Watz]

Dear All

The laboratory of Magnus Wolf-Watz at Umeå University is searching a motivated 
postdoc with an interest in enzyme dynamics. We use diverse techniques to 
address enzymatic rate enhancements from the perspective of enzyme dynamics. 
The candidate should either hold or expect to hold a Ph.D. in the area of 
biochemistry or structural biology, with expertise in either NMR spectroscopy 
or X-ray crystallography. Our department is equipped with state of the art NMR 
spectrometers including an 850 MHz machine equipped with a cryo probe. 
Expertise in protein production and purification is required.

The postdoc position is a fellowship for 2 years. Please visit the lab website 
for more information: 
www.biostruct.umu.se/principal-investigators/magnus-wolf-watz/.
Send your CV with a brief research statement as well as 2-3 contacts for 
references to magnus.wolf-w...@umu.se  before 
the 1st of August

Thank you,
Magnus Wolf-Watz


---
Dr. Magnus Wolf-Watz
Professor
Umeå University
Chemistry Department
Phone:+46 90 786 76 90

Lab Home Page: www.biostruct.umu.se/principal-investigators/magnus-wolf-watz/




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[ccp4bb] Poster Abstract submission for 10th International Workshop on Radiation Damage to Biological Samples. Brookhaven National Laboratory, 13-14th September 2018

[Elspeth Garman]

Poster Abstract submission is now open (closes 17th August, Workshop 
registration deadline 31st August) for the 10th International Workshop on 
Radiation Damage to Biological Samples will be held at BNL, USA 13th-14th 
September 2018.
Further details can be found at:
https://www.bnl.gov/rd10/
and the confirmed speakers at:
https://www.bnl.gov/rd10/agenda.php
The Workshop will address essential questions and challenges of radiation 
damage to biological samples during their examination with ionizing radiation. 
The workshop will cover various X-ray and electron scattering techniques, from 
crystallography to imaging, and offers ample opportunities for information 
exchange and discussion among researchers from around the globe.
Sessions will cover:
1) Basic Understanding of Radiation Damage Mechanisms
2) Biological Studies Affected by Radiation Damage
3) Practical Aspects of Reducing Radiation Damage at Synchrotrons
4) Damage at New Sources - XFEL and 4th generation synchrotrons
5) Radiation Damage in Complementary Fields including Biological Imaging
Best wishes
Elspeth Garman
On behalf of the Organising Committee

Elspeth F. Garman,
Professor of Molecular Biophysics,
Senior Kurti Fellow, Brasenose College, University of Oxford
Postal address:
  Laboratory of Molecular Biophysics,
  Department of Biochemistry,
  University of Oxford,  Tel: (44)-1865-613297
  South Parks Road,  FAX: (44)-1865-613201
  OXFORD, OX1 3QU, U.K. E-mail: 
elspeth.gar...@bioch.ox.ac.uk
http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=garman
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