CONECT part in the pdb file

Question

[Elsaid]

I successfully wrote a new PDB file, and it consists of C,H and O(1000+). I can get three columns with the indices of three atoms separately. I'm looking for a rule for writing the CONECT part. Note: I am using Pandas.

Thanks

[Wayne]

https://www.wwpdb.org/documentation/file-format-content/format33/sect10.html
and
https://proteopedia.org/wiki/index.php/PDB_file#Bonds:_Connectivity

However, Pandas isn't going to have the chemical insight to generate those as was hinted at by @Mensur Dlakic here:

"I can state with certainty that pandas is not the best tool for editing PDB files."

Are you sure you need the conect records? Many viewers don't need the connect part as summarized at the Proteopedia link I supplied:

"Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 Ångstroms of each other are deemed to be covalently bonded."

Some viewing or modeling software are able to generate connect records, such as PyMOL, Swiss PDBViewer/DeepView, and Chimera.

[Elsaid]

Thanks for your reply! I will check some of the software.