Re: [ccp4bb] Some ccp4i2 menu options seem missing.

[Jonathan Cooper]

[SOLVED] Sorry folks, that was an easy one, "Clone Job" sorted it. Thanks for 
the tip Huw.

Sent from Yahoo Mail on Android 
 
  On Wed, 24 Apr 2019 at 23:14, Huw 
Jenkins<288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote:   Hi,

> On 24 Apr 2019, at 22:42, Jonathan Cooper 
> <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Any clues much appreciated, otherwise I'm back to the old gui.

The linux one looks like a job that has been run. If you got to the task menu 
and click on Refinement - REFMAC5 does the new job open up with those fields 
un-editable? If so which version of CCP4 is this?

Best wishes,


Huw


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Re: [ccp4bb] Some ccp4i2 menu options seem missing.

[Huw Jenkins]

Hi,

> On 24 Apr 2019, at 22:42, Jonathan Cooper 
> <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Any clues much appreciated, otherwise I'm back to the old gui.

The linux one looks like a job that has been run. If you got to the task menu 
and click on Refinement - REFMAC5 does the new job open up with those fields 
un-editable? If so which version of CCP4 is this?

Best wishes,


Huw


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[ccp4bb] Some ccp4i2 menu options seem missing.

[Jonathan Cooper]

Hello, on linux (Lubuntu) my install of the latest ccp4i2 does not allow me to 
change certain options, e.g. from isotropic to anisotropic refinement: 
www.ucl.ac.uk/~rmhajc0/jbc.jpg

whereas my spy with a Mac gets:
www.ucl.ac.uk/~rmhajc0/jg.jpg

and the desired options are there and working. 
Any clues much appreciated, otherwise I'm back to the old gui.
Best wishes
Jon Cooper



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[ccp4bb] Scientist/Investigator BioNMR position - Novartis

[Bussiere, Dirksen]

Colleagues:

This might be a bit off-topic, but is still biophysics related.  We are looking 
for a research associate or investigator to join our group in the area of 
biological NMR.  The job advertisement follows, as does the link which will 
allow you to apply.   Please don't send me your CV, rather apply online.  
However, I am happy to answer questions.  The advertisement follows.

-Dirk

Dirksen Bussiere, Ph.D., M.B.A.
Director, Structural and Biophysical Chemistry / NLS
Novartis Insts. for BioMedical Research
5300 Chiron Way
Emeryville, CA 94608-2916
dirksen.bussi...@novartis.com

  The Emeryville Structural Based Drug Design (SBDD) Center, co-localized with 
the Novartis Institute for Tropical Diseases (NITD) in the San Francisco Bay 
Area, is seeking a self-motivated research scientist with expertise in 
Biomolecular NMR spectroscopy or a related biophysical or analytical method to 
join our Structural & Biophysical Chemistry group. The successful candidate 
will be an integral member of local and global structure-based drug discovery 
teams and will support our efforts to develop innovative medicines for various 
therapeutic areas like oncology, immuno-oncology, cardiovascular, respiratory, 
auto-immune, neurological and tropical diseases.

Your Responsibilities
* Prepare Bio-NMR samples as well as record and analyze spectra of proteins, 
peptides, nucleic acids and small molecules
* Independently interpret data and present results to internal project teams 
and global stakeholders to help drive our drug discovery projects
* Develop and/or implement new NMR assays to probe the structure, dynamics and 
interactions of biomolecules and ligands
* Maintain an in-house Bio-NMR laboratory consisting of high-field 
spectrometers with associated computing and robotics
* Perform lab and office duties, such as ordering reagents, organizing 
inventories and keeping experimental records
* Contribute intellectually to structure-based drug discovery projects and 
collaborate with partners from other disciplines like disease biology, 
biochemistry, chemistry, bioinformatics, and IT
EEO StatementThe Novartis Group of Companies are Equal Opportunity Employers 
and take pride in maintaining a diverse environment. We do not discriminate in 
recruitment, hiring, training, promotion or any other employment practices for 
reasons of race, color, religion, gender, national origin, age, sexual 
orientation, marital or veteran status, disability, or any other legally 
protected status.
Minimum requirements* A B.A. or an advanced degree in Biochemistry, Chemistry, 
or Molecular Biology, or related discipline
* At least 3 year (M.S.) or 5 years (B.A.) of work experience in the 
pharmaceutical industry or academic research labs with demonstrated success in 
the application of biophysical techniques
* Extensive hands-on experience in two or more of the following biophysical 
techniques: NMR, SPR, BLI, MS, ITC, DSF, AUC, MST, CD
* Successfully demonstrated initiative, teamwork, collaboration and can-do 
attitude
* Flexibility to accommodate to rapidly changing priorities and deadlines, with 
strong interpersonal, written & oral communication, and problem-solving skills

Desired Skills
* Biomolecular or Analytical NMR spectroscopy using proteins, nucleic acids or 
small molecules is highly desired, but necessary additional training will be 
provided
* Experience in relevant structural biology / biophysics software, e.g. Pymol, 
Topspin or Prism is highly desired
* Knowledge of fragment-based drug discovery approaches is a plus, as is prior 
industry experience
* Basic or advanced programming language skills, e.g. Python, Julia or R, is a 
plus

Link to description and to apply:  
https://www.novartis.com/careers/career-search/job-details/266811BR





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Re: [ccp4bb] “Bound ligand” versus “modified residue”

[Nigel Moriarty]

The "CYS with" means that the main chain is restrained and treated the same
as "normal" CYS.

However, I'm not sure how the sequence should be handled in the file
especially mmCIF. Maybe John Berrisford can comment.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov


On Wed, Apr 24, 2019 at 10:27 AM Pavel Afonine  wrote:

> Hi Ian,
> perhaps there are as many answers to this as many subscribers to this
> list, but personally "Cysteine with attachment" seems more logic and clear
> to me than calling the whole thing a different name. Although I would also
> understand arguments like if it is a CYS with an attachment it is not
> really CYS any more and perhaps should be called a unique name. From
> refinement viewpoint both a fine.
> Pavel
>
> On Wed, Apr 24, 2019 at 8:59 AM Ian Clifton 
> wrote:
>
>> Hello everyone,
>>
>> PDB structure 4qdu contains a “modified residue”, 30V. This is joined
>> into the rest of the main chain by means of LINK records. In 5kwj, a
>> similar type of modification is described as a cysteine with a
>> side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
>> two clear examples we found to illustrate the question.)
>>
>> Is there any reason to prefer one of these approaches over the other?
>> Does it just depend on what ligands are already in the PDB?
>>
>> Thanks,
>> --
>> Ian Clifton ⚗ ℡: +44 1865 275677
>> Chemistry Research Laboratory ℻: +44 1865 285002
>> Oxford University 📧: ian.clif...@chem.ox.ac.uk
>> Mansfield Road   Oxford OX1 3TA   UK
>>
>>
>> 
>>
>> 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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>



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Re: [ccp4bb] “Bound ligand” versus “modified residue”

[Pavel Afonine]

Hi Ian,
perhaps there are as many answers to this as many subscribers to this list,
but personally "Cysteine with attachment" seems more logic and clear to me
than calling the whole thing a different name. Although I would also
understand arguments like if it is a CYS with an attachment it is not
really CYS any more and perhaps should be called a unique name. From
refinement viewpoint both a fine.
Pavel

On Wed, Apr 24, 2019 at 8:59 AM Ian Clifton 
wrote:

> Hello everyone,
>
> PDB structure 4qdu contains a “modified residue”, 30V. This is joined
> into the rest of the main chain by means of LINK records. In 5kwj, a
> similar type of modification is described as a cysteine with a
> side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
> two clear examples we found to illustrate the question.)
>
> Is there any reason to prefer one of these approaches over the other?
> Does it just depend on what ligands are already in the PDB?
>
> Thanks,
> --
> Ian Clifton ⚗ ℡: +44 1865 275677
> Chemistry Research Laboratory ℻: +44 1865 285002
> Oxford University 📧: ian.clif...@chem.ox.ac.uk
> Mansfield Road   Oxford OX1 3TA   UK
>
>
> 
>
> 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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[ccp4bb] Protein Crystallography Summer School at York, 1-7 September 2019

[Johan Turkenburg]

This year the University of York will be hosting a Protein Crystallography
Summer School, sponsored by CCP4 and others, which will take place 1-7
September. (This school has previously been held biennially in St Andrews.)



The course aims to cover the theoretical and practical aspects of protein
crystallography from protein expression and purification, through crystal
growth to data collection on in-house and synchrotron sources, phasing
methods, automated model building and phase extension, refinement, and
validation. Hands-on sessions in data processing (XIA2, DIALS), molecular
replacement, MAD/SAD phasing, refinement and electron density map
interpretation (in COOT) will be included.



The School is intended for postgraduates or postdocs new to
crystallography. The week is very intensive, and gives a concentrated
overview of the methods which many find useful.



As in the past, priority is given to UK applicants because of the funding
arrangements, but is open to a limited number of overseas applicants.



For further details and the application form please see
https://synergy.st-andrews.ac.uk/proteincrystallography/



Tracey Gloster (University of St Andrews)

Johan Turkenburg (University of York)



-- 
Dr. Johan P. Turkenburg X-ray facilities manager
York Structural Biology Laboratory
University of York
York YO10 5DD   UK  Phone (+) 44 1904 328251
http://orcid.org/-0001-6992-6838
EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm




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[ccp4bb] “Bound ligand” versus “modified residue”

[Ian Clifton]

Hello everyone,

PDB structure 4qdu contains a “modified residue”, 30V. This is joined
into the rest of the main chain by means of LINK records. In 5kwj, a
similar type of modification is described as a cysteine with a
side‐chain LINK to its “bound ligand”, 6Y3 . (These structures are just
two clear examples we found to illustrate the question.)

Is there any reason to prefer one of these approaches over the other?
Does it just depend on what ligands are already in the PDB?

Thanks,
-- 
Ian Clifton ⚗ ℡: +44 1865 275677
Chemistry Research Laboratory ℻: +44 1865 285002
Oxford University 📧: ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK




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[ccp4bb] 2 positions around XChem-related compound design

[Frank von Delft]

Dear all, I have two open to work on fragment/XChem-related methodology 
for structure-based compound design.


Team Leader (applications close next *Weds 1st May*):  full ad here 
, 
summary:


   /We are recruiting an experienced computational chemist or
   scientific programmer, to head the Fragalysis project for automating
   fragment hit progression, part of the XChem collaboration between
   SGC and Diamond...  The //Fragalysis
   //project leader will be tasked
   with converting the existing proof-of-concept tool into a
   production-level system that is routinely usable for analysing XChem
   results and designing and acquiring follow-up compounds. This will
   entail setting the scientific direction and priorities of the
   project through close and continuous interaction with expert and
   novice users; coordinating a growing team of scientific programmers
   and contractors; liaising with and expanding a wide and
   international set of collaborators and contributors; securing
   further funding for the project; helping supervise students; and
   developing specific methodologies of their own./


Postdoc (closing *Weds 15th May*):  full advert here 
, 
this is a summary:


   /This role will be tasked with the design and acquisition of
   follow-up compounds based on fragment screening hits from the Target
   Enabling Package (//www.thesgc.org/tep
   //) and Ultra-DD (//www.ultra-dd.org
   //) programs. The successful candidate will
   coordinate experimental validation of the newly designed compounds
   with collaborating scientists in order to progress them towards
   potent molecules.
   /

Cheers
Frank


--
Prof Frank von Delft
Associate Professor Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)

Principal Beamline Scientist: I04-1
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)



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[ccp4bb] PhD program in Austria -HIRING NOW

[Oberer, Monika (m.obe...@uni-graz.at)]

Dear Colleagues,

The fully-funded PhD program "Molecular Metabolism - MOBILES" is currently 
hiring motivated PhD candidates for positions in Graz, Austria. Besides being a 
dynamic place for science, Graz is regularly ranked among the European cities 
with the best quality of living, and a lively student city, not far from 
mountains and Mediterranean. There are twelve open positions, including two on 
lipid transport and lipid metabolism (PIs Zangger, Oberer) using integrated 
structural biology approaches.

For more details please follow the link:
https://docfunds-molecular-metabolism.uni-graz.at/en/open-positions/


Best wishes,
Monika Oberer
Speaker doc.fund
MOLECULAR METABOLISM


Assoc. Prof. Dr. Monika Oberer
Institute of Molecular Biosciences - Structural Biology
University of Graz
Humboldtstrasse 50/3
8010 Graz
Austria

Email: m.obe...@uni-graz.at
Phone: ++43-316-380-5431
*





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[ccp4bb] AW: [ccp4bb] Off topic - French Press Accessories

[Hughes, Jon]

hi naza,
i wouldn't touch machines like that from the USA – their prices are too high 
and  their tolerances are miserable. we bought a made-to-measure French press 
(including various stainless-steel cells) from a REAL hydraulics manufacturer 
near here
https://watzhydraulik.de/en/
about 20 years ago, and everything's still working as perfectly as it did on 
the first day.
best,
j

Von: CCP4 bulletin board  Im Auftrag von Nazahiyah Rodzli
Gesendet: Mittwoch, 24. April 2019 03:55
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Off topic - French Press Accessories

Dear All,

Our lab is using the good old Thermo French press (FA-078A-picture attached) 
with a mini sample cell which has only 3.5 ml maximum sample capacity and 
planning to use for as long as it lasts. However, we are now in need of a 
bigger sample cell for our membrane protein work. Unfortunately, I have been 
made aware that Thermo has long since discontinued its support and delivery for 
such robust piece of equipment and for the obvious reason I couldn’t find a 
company locally that can provide this. Can anyone suggest if there’s a way I 
can get the larger sample cell (FA-032 40K Standard - second picture attached); 
or any lab that happens to have an extra piece of the accessory or no longer in 
use and willing to let go at a reasonable price?



Best regards,
Naza


___

Nazahiyah Rodzli, PhD (The University of Manchester)
Scientist
Structural and Applied Genomics
Malaysia Genome Institute
National Institutes of Biotechnology Malaysia
Jalan Bangi,
43000 Kajang,
Selangor, MALAYSIA


[X][Das Bild wurde vom Absender entfernt. Image result for thermo french press 
standard cell]



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[ccp4bb] AW: [ccp4bb] Off topic - French Press Accessories

[Linnert, Dr. Miriam]

Dear Nazahiyah,

there is a small german company which sells the the former Thermo French press 
further. There we got three years ago a new larger cell.

http://www.gheinemann.de/htu-digi-french-press.html

But I think unfortunately the homepage works so far only in german.
Hope I could help you.

Best regards
Miriam

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Nazahiyah Rodzli
Gesendet: Mittwoch, 24. April 2019 03:55
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Off topic - French Press Accessories

Dear All,

Our lab is using the good old Thermo French press (FA-078A-picture attached) 
with a mini sample cell which has only 3.5 ml maximum sample capacity and 
planning to use for as long as it lasts. However, we are now in need of a 
bigger sample cell for our membrane protein work. Unfortunately, I have been 
made aware that Thermo has long since discontinued its support and delivery for 
such robust piece of equipment and for the obvious reason I couldn’t find a 
company locally that can provide this. Can anyone suggest if there’s a way I 
can get the larger sample cell (FA-032 40K Standard - second picture attached); 
or any lab that happens to have an extra piece of the accessory or no longer in 
use and willing to let go at a reasonable price?



Best regards,
Naza


___

Nazahiyah Rodzli, PhD (The University of Manchester)
Scientist
Structural and Applied Genomics
Malaysia Genome Institute
National Institutes of Biotechnology Malaysia
Jalan Bangi,
43000 Kajang,
Selangor, MALAYSIA


[Image result for thermo french press standard cell][Image result for thermo 
french press standard cell]



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