[Chimera-users] Matching a small ligand to another

Divjak Maja Maja.Divjak at petermac.org
Tue May 5 18:53:55 PDT 2020

Hi Elaine,

Hope you're well!
I'm trying to match a Lewis Y tetrasaccharide PubChem CID 71308612 to a partial Lewis Y ligand in PDB 3eyv. I'm having a whole world of trouble. I understand that you have to select at least three atoms in each molecule and they have to be the same atoms in the same order in each  to do this. I've used the 'label' command to show the atom names and numbers on each molecule. I've tried shift + cntrl click to select the atoms manually and then the command 'match sel'. This gives me the error message 'At least one atom must be selected'. Not sure why this is happening. I also tried using the 'match' command, but I'm not sure what identifiers to use for the two molecules . The PubChem molecule is listed as (noID) under chains and the partial ligand in the PDB is part of chain H. So, if I want to use match #X c1, c2, c3, #Y c1, c3, c4 etc. I don't know how to identify the two molecules. Using match #noID and #H does not work. I'm using Chimera 1.13. Is it better if I convert to Chimera X please?

Thanks so much and best wishes,


Dr Maja Divjak 
BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS)
Biomedical Animator
Office of Cancer Research

Phone  +61 3 8559 5961
Email  maja.divjak at petermac.org
305 Grattan Street
Melbourne Victoria 3000

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