[ccp4bb] 2-years postdoc position on electron crystallography in Vienna

[Tim Gruene]

Dear all,

the Centre for Chemical structure Analysis at the University of Vienna
is offering a 2-years postdoc position. The project is a joint project
with the Detector group at the Paul Scherrer Institut. A JUNGFRAU
detector will be combined with a JEOL Transmission Electron
Microscope for advanced data collection and aims at reaching a new level
of data quality in ED.

Applicants should apply via the job portal
https://jobs.univie.ac.at/job/University-Assistant-postdoctoral/975913901 
before end of September 2023. A detailed job description and
requirements are available there, too.

We aim at starting the project in autumn this year, but are flexible by
a few months.

We look forward to ambitious applicants for an exciting project.

Best regards,
Tim Gruene

P.S.: yes, this is the same position as posted August 7th, with the
updated link to the job portal of the University of Vienna

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] postdoctoral position - time-resolved serial crystallography

[Przemysław Nogły]

Dear All,

We have an exciting opening for a postdoctoral position in my group at the 
Jagiellonian University to investigate photoreceptor proteins with 
time-resolved serial crystallography.

For details and applications:
https://www.nature.com/naturecareers/job/12803466/postdoctoral-researcher-at-the-dioscuri-centre-for-structural-dynamics-of-receptors/?LinkSource=PremiumListing
Closing date is 15.09.2023

Best regards,
Przemek

Przemyslaw Nogly, Ph.D.
Group Leader of the Dioscuri Centre for Structural Dynamics of Receptors
Faculty of Biochemistry, Biophysics and Biotechnology
Jagiellonian University
Gronostajowa 7, Room C041
30-387 Kraków, Poland
+48 12 664 6339
https://noglylab.eu/
 [https://noglylab.eu/]



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Re: [ccp4bb] How to make covalent bond for modified nucleic acid

[FULVIO SACCOCCIA]

You May try "Builder" panel embedded in Pymol to make covalent bond.
Best
 Fulvio

Inviato da Outlook per Android


Da: CCP4 bulletin board  per conto di Hsuan-Ai 

Inviato: lunedì, agosto 28, 2023 6:54:01 PM
A: CCP4BB@JISCMAIL.AC.UK 
Oggetto: [ccp4bb] How to make covalent bond for modified nucleic acid

Greeting to all,

I am struggling to place modified nucleotides into an oligonucleotide strand. I 
built the ligand restraint dictionaries both in Acedrg or Elbow; the generated 
liogands look fine, but the covalent bond between the ligand and the 
modification site cannot be generated, also in vain when following the Acedrg 
tutorial (where additional covalent bond restraint was generated). I also tried 
to edit the pdb file directly by specifying which atom links to which. It, 
nevertheless, did mot work as I imagined.

How do you usually make ligand link to protein / nucleic acid via covalent 
bond? Is there some trick to tell the program the existence of covalent bonds? 
Any suggestions are heartily appreciated. Thank you in advanced!

Best regards,
Ai



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Re: [ccp4bb] How to make covalent bond for modified nucleic acid

[Keitaro Yamashita]

Dear Ai,

Are you trying to make phosphodiester bonds in the main chain? Do your
modified nucleotides follow the standard atom names (P, OP1, OP2, ...,
O3')? If so, you can just change the group name (_chem_comp.group) to
RNA (or DNA). Otherwise you could either change atom names to follow
the standard, or make link dictionary cif files (using acedrg -L). The
link dictionary would be needed for all combinations that happen in
the model, so following the standard could be a better solution.
However, it depends on what type of modifications your nucleotides
have.

If it's not a phosphodiester bond, the link dictionary cif file will
need to be created.

Best regards,
Keitaro

On Mon, 28 Aug 2023 at 17:54, Hsuan-Ai  wrote:
>
> Greeting to all,
>
> I am struggling to place modified nucleotides into an oligonucleotide strand. 
> I built the ligand restraint dictionaries both in Acedrg or Elbow; the 
> generated liogands look fine, but the covalent bond between the ligand and 
> the modification site cannot be generated, also in vain when following the 
> Acedrg tutorial (where additional covalent bond restraint was generated). I 
> also tried to edit the pdb file directly by specifying which atom links to 
> which. It, nevertheless, did mot work as I imagined.
>
> How do you usually make ligand link to protein / nucleic acid via covalent 
> bond? Is there some trick to tell the program the existence of covalent 
> bonds? Any suggestions are heartily appreciated. Thank you in advanced!
>
> Best regards,
> Ai
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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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