Hi Julie Ta.
Do you know if there’s an API (pref. Python 3.9 or later) for downloading the 3D coordinates from ChemSpider? Harry > On 6 Dec 2022, at 12:04, Julie Tucker > <000020908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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 <oliver.s.sm...@gmail.com> wrote: > 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 > > There > > https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519 > > > Provides a SDF file. > > Hope this helps > > Oliver > > p.s. I you are stuck with ChEBI identifiers it would be possible to > programatically find the equivalent PubChem CID. > > > > >> On 6 Dec 2022, at 11:31, Harry Powell >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> 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 small molecule structures, but something around >> 1.395Å rings a faint bell). >> >> I need to have ligands that have realistic sizes, and while I’m perfectly at >> ease scaling the models to what I think are sensible sizes, I can’t help but >> think that this isn’t necessary and I’ve missed something somewhere. >> >> Here’s an example of a molecule that I used this morning - >> >> >> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0 >> >> contents of downloaded file - >>> >>> Marvin 01140911122D >>> >>> 15 15 0 0 0 0 999 V2000 >>> -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> -0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 1.4992 0.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >>> 1.4992 -0.6675 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >>> 1.9841 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> -1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.0001 1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0.0001 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 1.7541 1.4520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> -1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >>> 2.0809 -1.5365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 >>> 10 1 2 0 0 0 0 >>> 1 2 1 0 0 0 0 >>> 14 2 1 0 0 0 0 >>> 8 3 1 0 0 0 0 >>> 4 3 2 0 0 0 0 >>> 7 4 1 0 0 0 0 >>> 1 5 1 0 0 0 0 >>> 5 3 1 0 0 0 0 >>> 12 5 1 0 0 0 0 >>> 6 2 1 0 0 0 0 >>> 6 4 1 0 0 0 0 >>> 11 6 2 0 0 0 0 >>> 9 7 1 0 0 0 0 >>> 13 7 1 0 0 0 0 >>> 9 8 2 0 0 0 0 >>> M END >>> >> >> Harry >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > -- > Julie Tucker > York Biomedical Research Institute > Department of Biology and HYMS > University of York > > My normal working days are Monday-Tuesday and Thursday-Friday. Please be > patient if you do not hear from me promptly. I choose to work flexibly; > please only respond to this message when convenient for you to do so. > > Email disclaimer > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
