[ccp4bb] NCCAT-NCITU 2023 CryoET short course - Application deadline Jan 1, 2023 - NYC, USA

Dear all, A reminder the registration deadline for the NCCAT-NCITU cryoEM short course in tomography is January 1, 2023 at 5 pm ET. The workshop will be held April 10-14, 2023 at the New York Structural Biology Center in NYC. Accepted applicants will be informed by mid-late January 2023. This

[ccp4bb] Register Now: Instruct-ERIC Structure Meets Function Webinar - 13 December 3PM CET

Dear all, Registration is now open for the 23rd edition of the Structure Meets Function webinar from Instruct-ERIC. The webinar will take place 13 December 2022 at 12:00 ART (15:00 CET). This month will feature two excellent speakers, both from

Re: [ccp4bb] ChEBI and SMILES

Please see https://gitlab.com/-/snippets/2468156 an extension that downloads SDF files > On 7 Oct 2022, at 10:12, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Probably a silly question, but I was wondering how to

Re: [ccp4bb] ligands found in ChEBI...

Maybe more information on that here: https://developer.rsc.org/? I'm not an expert and only used it interactively... Julie On Tue, 6 Dec 2022 at 12:19, Harry Powell wrote: > Hi Julie > > Ta. > > Do you know if there’s an API (pref. Python 3.9 or later) for downloading > the 3D coordinates from

Re: [ccp4bb] ligands found in ChEBI...

Hi Oliver I’d just worked that out when I tried an obviously non-planar molecule (that I didn’t include with my breakfast this morning)! PubChem looks like a useful way forward - many thanks. Harry > On 6 Dec 2022, at 11:55, Oliver Smart wrote: > > Hi Harry, > > The SDF found at ChEBI is a

Re: [ccp4bb] ligands found in ChEBI...

Chemspider can also provide you with a .mol file amongst other things. http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194 Best wishes Julie On Tue, 6 Dec 2022 at 11:55, Oliver Smart wrote: > Hi Harry, > > The SDF found at ChEBI is a 2D SDF with the

Re: [ccp4bb] ligands found in ChEBI...

Hi Harry, The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. I do not think that ChEBI has 3D coordinates. Why not use PubChem instead as this does provide 3D sdf files? For your caffeine example: https://pubchem.ncbi.nlm.nih.gov/compound/64119

Re: [ccp4bb] ligands found in ChEBI...

Whoops. It looks like these entries are not supposed to be 3D models, but representations of 2D line drawings (which I noticed when I had a look at an obviously non-planar molecule). Which is a shame, because I was hoping I could use them in 3D modelling… Sorry for polluting your inboxes!

[ccp4bb] ligands found in ChEBI...

Hi folks Can anyone help with this? I must have missed something in the documentation, because I don’t understand why the .mol and .sdf files downloaded from https://www.ebi.ac.uk/chebi seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now since I solved any