Pdb file help: renumber residue manually

Question

[a.garcon.a]

Hello,

I am currently working on a protein structure and I would like to change the residue number of some solvent atoms (Zn ions).

My protein is a trimer and some Zn atoms present the same symmetry (that is, residue X of chain A,B,C are all connected to a Zn atom). For example, Zn atoms #1, #17 and #20 are liked to residues #537 in chain A,B and C.

I would like to rename those atoms #101, #102, #103 in the pdb file to make it more easy to read. All my Zn atoms are in a special chain Z.

I am working with Coot, but it only allows to shift the residue numbers by a given offset (useless in my case). When I try to modify manually those number (opening the pdb file using wordpad), coot does not like the new format and messes up with all the atom numbers.

Could anyone explain me how to manually change those number please? I think I might not be using the correct text editor.

Thank you!

Antoine

Answer 1

[alolex]

Since you are using wordpad I'm assuming you are on a windows machine. Try using Notepad instead and do not save it with any rich text encoding as this will add additional invisible characters (so check your default save settings). If you have access to a mac/unix/linux machine I suggest using that instead of windows, and edit the file using the terminal with a program like nano or vim. Also, make sure you are not adding any tabs or extra spaces at the end of your lines. If all of that checks out then it may be the number change itself that is messing things up. In that case you will need to study your file and the accepted PDB format specifications to figure out what the issue is.

[a.garcon.a]

Thanks a lot. I am currently on a Windows machine and do not have access to my usual Ubuntu.

Somehow every Windows text editors are messing with the pdb format (when saving I think). I solved the problem downloading the Pc version of Gedit.

Thanks for your tips!