Help:Modify A PDB File

From Proteopedia

This page explains some ways to modify a PDB file in order to use it to show what you want to show.

Merging two (or more) PDB files

Often in Proteopedia, we want to show two or more models superimposed on each other. Currently, the best way to accomplish this in Proteopedia is to superimpose your structures using an external program (or by hand using a text-editing program), save your resulting multi-model or multi-chain PDB file, upload it into Proteopedia, and then load it in an applet or a scene on your Proteopedia page.

Using PyMOL

PyMOL makes it simple to superimpose two PDB files and save them as one PDB file, we just have to be careful to check the chain names so that both PDB files don't end up having the same chain name in the resulting merged file.

1. load the PDB files into PyMOL and align them if desired (align by clicking on the "A" button next to one of the object's names in the right hand toolbar and choosing align->to molecule->pick the 2nd molecule)
2. if the PDB files are both one-chain objects and both have the same chain name, you should set it so that they have different chain names by changing one of the model's chain names in PyMOL by typing "alter object01, chain='B' " in the command line, where "object01" is the name of the object whose chain name will be changed (you can see the object names on the right hand toolbar in the PyMOL graphical user interface), and where "B" is the chain letter that you want to set for that object's chain. (Note: dealing with objects with multiple chains is not yet explained here. If you know how to rename only one chain of a multichain object in PyMOL, please add that explanation here.)
3. now that the PDB files have different chain names, select both objects by typing "select all" into the PyMOL command line and pressing enter. All atoms should be part of one selection called "(sele)"
4. click on the "A" button next to the selection ("(sele)") in the right hand toolbar of the graphical user interface of PyMOL and then select "copy to object". A new object will be created that merges
5. save your new object consisting of two aligned, superimposed molecules by going to "File->Save molecule.." and choosing your new object name (it will probably be called "obj01") and saving it.
6. upload the resulting saved file to Proteopedia and you may then use it in applets and in scenes in Proteopedia