[ccp4bb] Two postdoc positions in Ubiquitin Signalling, WEHI, Melbourne, Australia

and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Officer---Structural-Biology-of-E3-Ubiquitin-Ligases_JR1578-3 Contact: Dr. Bernhard Lechtenberg, lechtenber...@wehi.edu.au<mailto:lechtenber...@wehi.edu.au> The Komander lab seeks to recruit a postdoc with stru

Re: [ccp4bb] To Trim or Not to To Trim

eases Case Western Reserve University Cleveland, OH 44106 https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg <968307750321-dmarc-requ...@jiscmail.ac.uk<mailto:968307750321-dmarc-requ...@jiscmail.ac.uk>

Re: [ccp4bb] To Trim or Not to To Trim

Hi Rhys, I am also all for leaving side chains and letting the B-factors deal with the weak/absent density. I don’t think there is a consensus, but I kind of remember that somebody did a poll a few years ago and if I remember correctly the main approaches were the one described above, or trimm

Re: [ccp4bb] Postdoc opportunity at WEHI, Melbourne, Australia

From: Bernhard Lechtenberg Date: Thursday, 9 February 2023 at 11:04 am To: CCP4BB@JISCMAIL.AC.UK Subject: Postdoc opportunity at WEHI, Melbourne, Australia Dear colleagues, My lab is looking for a Research Officer (Postdoc) to strengthen our team in the Ubiquitin Signalling Division at WEHI in Mel

[ccp4bb] Postdoc opportunity at WEHI, Melbourne, Australia

Dear colleagues, My lab is looking for a Research Officer (Postdoc) to strengthen our team in the Ubiquitin Signalling Division at WEHI in Melbourne, Australia. We aim to understand the structure and molecular mechanisms of E3 ubiquitin ligases, their basic biology, and roles in human diseases

Re: [ccp4bb] A Problem of my Research Protein

Hi Guohui, Are you sure this is caused by disulfide bond formation? Do you have any reducing agent in your buffer? 5 Cys residues in 30 amino acids looks very much like a zinc finger to me. Is there any evidence for that? Are there any other zinc binding residues, i.e. His in this region? Good

Re: [ccp4bb] Cell disruption

eck the instrument for free . I have had this one for 10 years in my lab now. And before that was using one for 7 years during my post doc. I would not lyse bacteria by any other method now. I hope this helps. All the best. Pascal On Sat, Aug 15, 2020 at 9:08 PM Bernhard Lechtenberg mailto:lec

[ccp4bb] Cell disruption

Dear colleagues, We are currently looking to purchase a cell disruptor/homogeniser mainly for routinely processing a few 100 mls of E. coli suspensions. With the current COVID-19 restrictions it is very difficult for us to test any equipment. I thus hope that some of you can share their experie

Re: [ccp4bb] Coot "Fix nomenclature error" window

Dear Evgenii, The following from the Coot manual should help: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#set_002dnomenclature_002derrors_002don_002dread add “set-nomenclature-errors-on-read ignore” to your Coot startup file. In case you are using they python file, e.

[ccp4bb] Job posting - CryoEM Research Group Leader in Australia

Dear colleagues, We would like to bring to your attention a job opening for a Research Group Leader specialising in CryoEM at the The Walter and Eliza Hall Institute of Medical Research in Melbourne Australia. For details see - https://www.wehi.edu.au/cryoem-laboratory-head This is a 7-year ap

Re: [ccp4bb] covalent link to aa

Hi Markus, Did you load the .cif file into Coot before real space refinement? File -> Import CIF dictionary … When you do that, Coot should be able to refine the link and that might then also help for the refinement in Refmac. Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Associate Riedl L

Re: [ccp4bb] Na-Binding Protein?

Dear Jacob, The protease thrombin is another example. Thrombin is activated by Na+ (but not Li+ or K+). We have shown using NMR that Na+ binding allosterically stabilizes active conformations of thrombin. Additionally, numerous crystal structures of Na+-free (“slow” thrombin) and Na+-bound (“fa

Re: [ccp4bb] C-terminal amide

HI Abhisek, I had the same problem a few years back. Here is the solution I came up with thanks to help from the CCP4bb: 1) Add pointer atom in Coot NH2 and create link to C-terminal residue (Coot: Extensions -> Modeling -> Make link) 2) create cif file with correct link description (see below)

Re: [ccp4bb] Database for peptides in pdb format

Hi, if you just want a dipeptide, the easiest is probably to build one in PyMOL: Build -> Residue -> Leucine then Proline. You can save it in PDB format using File -> Save Molecule… You can probably do the same in Coot or JLigand if you want to use CCP4 programs. Hope that helps, Bernhard Be

Re: [ccp4bb] off topic - UV absorbance of phosphotyrosine

Hi Will, I previously used an extinction coefficient of 600M-1cm-1 for phosphotyrosine at 280nm estimated from figure 2 of this publication: http://www.ncbi.nlm.nih.gov/pubmed/2418612 Hope that helps, Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Fellow Riedl Lab Sanford-Burnham Medical

[ccp4bb] Fwd: [ccp4bb] Add C-terminal amide - solved

in Refmac with cif as LIB in Thanks especially to Maike and Augen Bernhard Begin forwarded message: From: Bernhard Lechtenberg mailto:blechtenb...@sanfordburnham.org>> Subject: [ccp4bb] Add C-terminal amide Date: October 29, 2013 6:32:37 PM PDT To: mailto:CCP4BB@JISCMAIL.AC.UK>&

[ccp4bb] Add C-terminal amide

Hello experts, I am currently working on a structure of a protein-peptide complex. The peptide was synthesized with a C-terminal amide group. What is the best way to add this in Coot and refine in Refmac? I did a search on the web but only found a protocol for CNS not for Coot/Refmac. Thanks f

[ccp4bb] Problems with key bindings in coot0.7.2 CCP4 install

Hi all, I recently installed CCP4 6.4 under Mac OS X 10.8.5 and now have problems using key bindings in the Coot version (0.7.2) that comes with CCP4. Although most of the standard key bindings still work, some of them (e.g. 'o' for other NCS chain) and most of the user-defined key bindings do

Re: [ccp4bb] Win-coot: replace residue

Hi Uma, when I do the same procedure (in OSX, but the problem seems to be the same), the new residue is stored in a new chain with residue number 1. So you would need to renumber the residue and change the chain ID back to the original chain ID. It's annoyingly complicated, but it works for me.

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

Hi Donghui, I don't think that is a problem in PyMOL. The cartoon representation is an idealized form of the secondary structure and does not strictly follow the atomic coordinates of the protein backbone. The strands are flattened and that's why you see the gaps between the strand and the side

Re: [ccp4bb] Coot chain ID

In Coot you can use Extensions -> Modelling -> Reorder Chains Bernahrd -- Bernhard Lechtenberg PhD student Huntington lab University of Cambridge Department of Haematology Cambridge Institute for Medical Research Wellcome Trust/MRC Building, Hills Road Cambridge, CB2 0XY United K