If a residue is not recognized by the 3D-SNFG program, consider manually adding it to the script. Open the downloaded file (vmd.rc, .vmdrc, or 3D-SNFG.tcl) using any text editor. The residue names are defined towards the beginning of the script. It starts with Glucose and ends with Psicose, so the easiest way to find the top of the list is to search for ‘Glc’. The residues are divided into the three nomenclatures from which they were sourced. Simply insert the residue name into the corresponding list. For example, adding a glycam name (1GB) to the list would change the following:
set Glc_common [list GLC MAL BGC] set Glc_charmm [list AGLC BGLC] set Glc_glycam [list 0GA 0GB 1GA]
set Glc_common [list GLC MAL BGC] set Glc_charmm [list AGLC BGLC] set Glc_glycam [list 0GA 0GB 1GA 1GB]
Note that Glc_common refers to PDB nomenclature.
If you consider a residue name as common, and would like to include it in future updates, please contact us.