Hi,
I have three separate pdb (protein databank) files that each represent a different segment of my protein (ex. pdb1 has residues 1-20, pdb2 has residues 20-80 and pdb3 has residues 80-100) and I want to connect these to form one pdb file (pdb4 to have residues 1-100). Also note that I want to keep the secondary structure defined in my "middle" pdb file (pdb2). Can Pymol "attatch" my 3 pdb files? If so, how can I do this? I'm new to Pymol so any help would be greatly appreciated.
Thanks,
Thomas
Hi, Thomas.
Before reading on. If you message me privately with an email address I will reply and have a crack at this for you with the .pdb files which you could send over and provide some info on how it should look. Otherwise...
Yes this is possible in a crude way. When you load the .pdb files do they load on top of one another to do they load in the correct positions next to one another?
PyMOL has two main modes. Viewing mode and Editing mode. In the bottom right hand corner there is some green text that reads "Mouse Mode" and some red text next to it that defaults to "3-Button Viewing". Clicking on the red text will toggle between the viewing mode and "3-Button Editing".
If your three molecules/fragments load in the wrong position and orientation relative to one another, open them all in PyMOL. Change to "3-Button Editing" mode. Then if you press Left Shift + Middle Mouse on one of the molecules/fragments you will be able to drag it around in virtual space. Left Shift + Left Click allows you to rotate the entire molecule. Once you have got them in the correct relative positions and then change back to "3-Button Viewing" mode.
Before you can add a covalent bond you need to move all the fragments to the same "Object". In the right hand pane, click the A button next to one of the fragments. Mouse over "copy to object" and click to select the object you want to copy it too. i.e. one of the other fragments. Repeat so that all the fragments are in one object. Note that PyMOL will literally duplicate the entire fragment in the new Object... You can delete the original fragment that you started with from PyMOL and its duplicate will remain.
Next you want to add a covalent bond between the molecules/fragments. To do this, double check first you are in "3-Button Viewing" mode, then display everything as sticks or ball and sticks by pressing the S button next to "all" on the right hand pane and clicking the appropriate display mode. Then press Left Ctrl + Middle Click on the two atoms you want to bond. You should see a little grey filigree sphere icon encircle each of the two atoms. Pressing Left Ctrl + Middle Click on them again will de-select them. Once you have selected them both, in the command line type:
bond pk1,pk2, 1
this will draw a single covalent bond between the two atoms. Changing the number at the end of the string changes the bond type. 2 is a double bond and so on. If you make a mistake press Left Ctrl + Middle Click on the two atoms and type
unbond
in the command line. Once you've done click "File" "Export Molecule" "Save" and then chose the .pdb option from the list of file types.
If all of the fragments load in the correct relative position just repeat the steps regarding bonding the atoms together after loading them all into PyMOL.
As shown above it can be done, but the orientation of each fragment is unknown so be aware that your final depiction is just that - a picture, and not necessarily how the real thing should look. These are however very short fragments, and perhaps you have evidence of interactions - when I did this with larger fragments, I had the advantage of data from SAXS experiments to which I could fit my final construct.
Thomas,
Open your pdb2 first in the PyMOL window
- open the other PDB file
- select merge with the current session
Repeat.
Finally, save the protein in PDB format.
Superimpose using spdbv or pymol or you can stitch both the fragments using Python programming.
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