Either Python scripts in the directory "icn3dpython" or Node.js scripts in the directory "icn3dnode" can be used to analyze structures in command line.

In your Node.js scripts, you can call iCn3D JavaScript functions in icn3d npm package. You can then run these scripts in command line with one second sleep time in between. Here show a few examples.

Install the following packages (The version of node should be 16 or later):

npm install three
npm install jquery
npm install jsdom
npm install icn3d

npm install axios
npm install querystring

• Ligand-Protein Interactions

  In the command line, run the following:

    node ligand.js 5R7Y JFM
  

  This finds the residues in the PDB structure "5R7Y" interacting with the ligand with a residue name "JFM". The output looks like the following:

    5R7Y, 5R7Y_A, 164, H, 3C-like proteinase, JFM
    ...
  

• Retrieve Annotations for PDB or AlphaFold Structures

  In the command line, run the following command with the annotation type defined as: "1" for SNPs, "2 for ClinVar, "3" for Conserved Domains, "4" for Functional Sites, "5" for 3D Domains, "6" for Interactions, "7" for Disulfide Bonds, "8" for Cross-Linkages, "9" for Post-Translational Modification (PTM), and "10" for transmembrane region.

    node annotation.js Q08426 1
  

  This retrieves the SNP annotations for the AlphaFold UniProt ID Q08426. It also works for any PDB ID. The output listed the residues with SNPs for each chain:

    Q08426_A        [{"Q08426_A_3":"3E>A"},{"Q08426_A_3":"3E>K"},{"Q08426_A_4":"4Y>H"}...
  

• Protein-Protein Interactions

  In the command line, run the following:

    node epitope.js 7BWJ E L
  

  This finds the residues in the chain "E" of the PDB structure "7BWJ" interacting with the chain "L". The output looks like the following:

    7BWJ, 7BWJ_E, 483, V, SARS-CoV-2 receptor binding domain, 7BWJ_L, 31, G, antibody light chain
    ...        
  

• Protein-Protein Interaction Details

  In the command line, run the following for a PDB structure:

    node interactiondetail.js 1KQ2 A B
  

  or the following for a custom PDB file:

    node interactiondetail2.js [filename] A B
  

  This outputs the residues in the chain "A" of the structure interacting with the chain "B". The output looks like the following:

    bondCnt: [
    {
    res1: '1KQ2_A_11_ALA',
    res2: '1KQ2_B_54_LEU:contact_1 ',     
  

  where "res1" is one of the residues in chain "A", "res2" is a list of interacting resiues in chain "B". Each residue has the format of [PDB]_[chain]_[residue number]_[residue name]:[interaction type]_[count of interaction].

• Protein-Protein Interactions Due to Mutations

  In the command line, run the following:

    node interaction2.js 6M0J E 501 Y
  

  This finds the change of interactions between the RDB domain (chain "E") of SAR-Cov-2 (PDB ID 6M0J) and ACE2 due to the mutation N501Y. The output looks like the following:

    6M0J, 6M0J_E, 501, N, Y, 0, 0, 9, 0, 1, 1
  

  where "0, 0, 9, 0, 1, 1" means the change of hydrogen bonds, salt bridges, contacts, halogen bonds, Pi-Cation interactions, Pi-Stacking interactions are 0, 0, 9, 0, 1, 1, respectively for the mutation N to Y at position 501.

• Detect Ig domains and assign IgStrand reference numbers

  You can download the folders "refpdb" and "tmalign-icn3dnode" to your local directoy, compile "tmalign-icn3dnode", and modify the script "refnum.js" to set up the path to the local program "tmalign-icn3dnode", then run the following:

    node refnum.js [a list of comma-separated PDB or UniProt IDs (no space)]
  

  The output JSON file contains the Ig domain detection, templates, reference numbers, etc. You could also specify a template in the folder "refpdb" to detect the Ig domains:

    node refnum.js [a list of comma-separated PDB or UniProt IDs (no space)] [a template, e.g., CD28_1yjdC_human_V.pdb]
  

• Output Secondary Structure in PDB or JSON

  In the command line, run the following:

    node secondarystructure.js [filename] [pdb or ss]
  

  [filename] is the name of your local PDB file, and [pdb or ss] is either "pdb" or "ss". "pdb" means to export the PDb file containing the secondary structure information. "ss" means to export the secondary structure information alone.

• Add Missing Atoms in the PDB file

  In the command line, run the following:

    node addmissingatoms.js [filename]
  

  [filename] is the name of your local PDB file. The command will fill the missing atoms in the PDB file, but it will not fill the missing residues.

• Show Domain and Site Information for a Protein

  In the command line, run the following:

    node cdsearch.js YP_009724390 hits
    node cdsearch.js YP_009724390 feats
  

  The first command finds the binding site information for the RefSeq protein "YP_009724390". The output looks like the following:

    YP_009724390    417     K       cd21480 SARS-CoV-2_Spike_S1_RBD 1       receptor binding site   6XR8,7CWL
    ...
  

  where "417" is the residue position, "K" is the residue name, "cd21480" is the domain ID, "SARS-CoV-2_Spike_S1_RBD" is the domain name, "1" is the site index, "receptor binding site" is the site type, "6XR8,7CWL" is the example PDB IDs.

  The second command finds the domain information for the RefSeq protein "YP_009724390". The output looks like the following:

    YP_009724390    62      V       pfam01601       Corona_S2       1       superfamily     6XR8,7CWL    
    ...
  

  where "62" is the residue position, "V" is the residue name, "pfam01601" is the domain ID, "Corona_S2" is the domain name, "1" is the index, "superfamily" is the domain type, "6XR8,7CWL" is the example PDB IDs.