[ccp4bb] Postdoc positions at Monash University

Hi All, I have 3 open postdoc positions in my group starting from March 2021. The work will focus on in situ structural biology (2x) and image processing/software development (1x). I am looking for people with experience in one or more of the following: cryoFIB, cryoET, CLEM. The software

[ccp4bb] Genentech Postdoctoral Fellowship – Structural Biology, Matsumoto Lab

Dear Colleagues, My lab, within the Structural Biology Department at Genentech, is seeking an innovative Postdoctoral Fellow to pursue engineering and structural characterization of immunoglobulins and their interactions with various cellular receptors and antigens. The Postdoctoral Fellow will

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

James, you know you can generate heat within the LAMP test, there’s chemistry for that and very accurate, sufficient for 30 - 45 minutes “runtime" But I enjoy reading your emails. Jürgen > On Dec 7, 2020, at 8:50 PM, James Holton wrote: > > > Yes, I would like to congratulate all these

Re: [ccp4bb] SARS-CoV-2 test on a smartphone

Yes, I would like to congratulate all these authors for getting this out. Many of them are friends and colleagues, and it is great to see them doing well, and getting this kind of work in front of as many eyes as possible.  The nice thing about this particular assay is that it is linear with

[ccp4bb] Recruiting Cryo EM Facility Manager

Dear Colleagues, The University of Texas Health Science Center at San Antonio is seeking an Assistant/Associate Professor (Research Track) to manage our new cryo-EM facility. The candidate will have the unique opportunity to be involved in development of the facility from its early stages

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

We have drifted far from the original topic of this thread and if we continue I'll just make more of a fool of myself. I'll just go back to the original topic that I started with, that encoding connectivity information into an ID is not reliable or sustainable in a relational database.

[ccp4bb] Submission Deadline on December 14th

Hi CCP4BB community, The AIMS Awards Fall 2020 application deadline is just one week away! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development programs, and get published. We encourage investigators, postdocs,

Re: [ccp4bb] how to swap chain IDs

Maybe sort_chains(imol) is what you want. Additionally or alternatively, change the order or the SSBOND or LINK header records. HTH. Paul. On 07/12/2020 18:59, Christian GALICIA wrote: Dear Folmer, Thank you for your answer. Only one out several chains is bound to a ligand in the

Re: [ccp4bb] how to swap chain IDs

Dear Folmer, Thank you for your answer. Only one out several chains is bound to a ligand in the structure, the aim is to convert the ligand-bound chain into chain A after suggestion of a reviewer. When I open the pdb file on a text editor I expect this chain to be listed before the other

Re: [ccp4bb] how to swap chain IDs

Dear Christian What exactly are you trying to accomplish? I don't quite follow why you would expect the atom positions to change? Unless I'm missing something? Also, why would you expect the numbering to change when you edit the chain ID? After CIF conversion: What do you mean by "original

Re: [ccp4bb] how to swap chain IDs

Hi Christian, couldn't you simply change the position in a text editor after changing chain IDs in coot? Atom IDs should renumber after reading and writing in coot, but conversion to cif will probably ignore the atom IDs anyway.  Greetings   Gottfried On Monday, 07-12-2020 at 19:19 Pavel

Re: [ccp4bb] how to swap chain IDs

Hi Christian, you can do it in Phenix PDBTools: GUI->Model Tools-> load files then Options->Other modifications look for Rename chain ID. Pavel On Mon, Dec 7, 2020 at 9:49 AM Christian GALICIA < christian.galicia.diaz.sant...@vub.be> wrote: > Hello, > I'm trying to swap the chain IDs of a

[ccp4bb] how to swap chain IDs

Hello, I'm trying to swap the chain IDs of a structure. I tried changing the IDs in coot and with PDBset, both change labels of the chains but not the atom positions nor numbering.Also, after the pdb file is converted to cif for deposition it displays in pymol in the original position making

[ccp4bb] Please help us improve our PDBe-KB aggregated views of proteins

Dear CCP4, To help us improve our PDBe-KB aggregated views of proteins, please fill in the following survey: https://tinyurl.com/y4vw8qkv The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org ) has recently

[ccp4bb] lookig for used crystallization devices

Dear All, We want to explore the possibility of acquiring a used Mosquito crystallization robot and/or Formulatrix imaging system to complement existing resources in our labs. In case you have any such systems in good condition, which you no longer need, we will be grateful if you can get in

Re: [ccp4bb] wsl2 Ubuntu 20.04

Dear Tim, Victor and Peter, Thank you for your quick reply! I found some of the posts you mentioned, but wasn't sure if it was related and how to change the parameters. For those googling after me: close your wsl distro in windows: make a file with a texteditor that is able to do a utf8 encoding

Re: [ccp4bb] wsl2 Ubuntu 20.04

Dear Johannes, On 07/12/2020 13:21, Tim Gruene wrote: Dear Johannes, w.r.t. shelx-binaries: you can check with #> cat /proc/cmdline whether the linux-kernel option include 'vsyscall=emulate'. Quite some time ago, the linux kernel made vsyscall obsolete. The SHELX-binaries are probably

Re: [ccp4bb] wsl2 Ubuntu 20.04

Dear Johannes, w.r.t. shelx-binaries: you can check with #> cat /proc/cmdline whether the linux-kernel option include 'vsyscall=emulate'. Quite some time ago, the linux kernel made vsyscall obsolete. The SHELX-binaries are probably compiled with an old compiler on an old linux system, and

[ccp4bb] wsl2 Ubuntu 20.04

Dear board, has anyone gotten ccp4 (specifically shelx and arpwarp) installed and working under wsl2 (windows subsystem for linux)? arp warp refuses to install with the following error: Segmentation fault *** ERROR *** This machine cannot run ARP/wARP executables that are statically linked to