[Chimera-users] Matching a small ligand to another

[Divjak Maja]

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,

Maja

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
www.petermac.org



Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee.  If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited.  Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you.  If you have received this email in error, please delete it and notify us immediately by telephone or email.  Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.