Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full structure in COOT, SWISS-PDBviewer or pymol?
Here is a link to the protein complex I am looking at
I would appreciate: Guidelines on how to do this (preferably in coot, pymol or Swiss-PDBviewer), or referral to a tutorial that actually goes through this would be great!
For reference: I found some descriptions on how to "build/merge" with Swiss PDB viewer here. And in threads from this discussion I found descriptions of how to do it with other molecular graphic tools as well (although I don't completely understand it)
What I have tried: In the tutorial for the SWISS-PDBviewer ( link ), I am able to follow some of the instructions, but I can't follow them for long:
- I upload three of the same PDB file in SWISS PDBviwerer (they are layered on top of each other)
- I can access/see the layers in the "layers info"
- I am told to open the "text icon" to see the PDB text file, and look for "mtrix" rows - which should come right before the "atom" rows. As cited from the instructions:
" Scroll down the pdb file until you find MTRIX lines (they are just before the ATOM lines). You can see 9 lines MTRIX. They represent three transformation matrices, and allow you to build the non-crystallographic symmetries of the protein"
I cannot find the "mtrix" rows in the PDB-text file, and am very unsure of how to follow the next instructions (link) after this as well. I am not able to click anywhere in the text file, then I get the error: "sorry can't recognize any clickable information under this pointer..
This is what I see above the "atom" row: