---------- Forwarded message ---------- From: Robbie Joosten <robbie_joos...@hotmail.com> Date: 2 Oct 2018 07:45 Subject: Re: [ccp4bb] Search by name on the PDB fails To: Murpholino Peligro <murpholi...@gmail.com> Cc:
Ligand-Expo is the place to be. It has search by name, identifier, SMILES and (my favourite, chemical formula). You can get the residue identfier there and then import the coordinates in COOT (get monomer). With the new CCP4 updates, most compounds in the PDB are defined in the CCP4 dictionary. If something is missing you can use the mmCIF compound definition from Ligand-Expo to generate restraints in AceDRG. Don't use the SDF file or a SMILES string unless strictly needed, because you won't get the correct atom names which will hurt in the long run. Cheers, Robbie On 2 Oct 2018 07:17, Murpholino Peligro <murpholi...@gmail.com> wrote: Hi all. I was searching for ligands/molecules at www.rcsb.org/pdb/ligand/chemAdvSearch.do<http://www.rcsb.org/pdb/ligand/chemAdvSearch.do> (middle tab in blue). If I try to search with the third option, i.e. "name" of the ligand/molecule, it never works. I tried tetraethylene glycol, nitric oxide, cisplatin and even the example provided biotin. Fortunately specifying the identifier (i.e. 3 letters..2 in some cases)... works. The problem is...what if I do not know the identifier? I was wondering if you know another database that might work better for me? (or you, if your brain works better with chemical names instead of identifiers) Ps If there is some sort of coordinate file, preferably pdb or xyz, to download that will be better. * Pubchem works with sdf files which I do not like because if I open the sdf file for biotin with pymol and then save it as pdb, and then open this on coot it looks strange... (png attached) (not sure if this is pymol's or coot's fault...but that's another thread I guess) Thanks ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
