Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear all, Thank you very much for all your messages. Unfortunately, I'm still on the same place, as yesterday... First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 1176355 containing FESAN molecule. Also, I prepared SMILES file based on SMILES of CB5 ligand (COSAN) ava

[ccp4bb] Structural Biology position at Odyssey Therapeutics (Boston MA)

Opportunity for a Senior/Principal Scientist at Odyssey Therapeutics in Boston MA. We are seeking a highly motivated and skilled Structural Biologist to join the Odyssey team at our site in Boston where you will be a key contributor to the structural enablement of pipeline discovery projects. Y

[ccp4bb] - Senior Principal Research Scientist, Protein Sciences / Structural Biology at Vertex Pharmaceuticals (San Diego, CA)

Hello all, Vertex https://global.vrtx.com/ is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious and life-threatening diseases. We discovered and developed the first medicines to treat the underlying cause of cystic

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, as previously suggested you can use AceDRG to generate a cif file for your ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL MOL2 files). You can use the AceDRG command line: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html or via ccp4i2, 'L

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Although it may not be apparent, there has been a lot of work going on in Acedrg development regarding Boron. One cannot say the same for Coot though and I can reproduce the behaviour reported by Rafa Dolot. If/when I can fix it, it will be available in 0.9.8.4. Paul. On 06/06/2022 13:24

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, In case you don't have a cif file for the ligand, I would load the SMILES expression into acedrg (or use any other input option) to create a cif file which you can then read into Coot. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Jun 6,

[ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear CCP4 Users, I am working with data containing a possible complex of protein with FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this ligand is not available in PDB. The closest molecule is COSAN (cobalt bis(1,2-dicarbollide)), which is labelled as CB5 and is available