Hi Sam, Sounds like you are doing the right thing. When you use menu entry File / Save PDB... there is a check-button at the bottom of the save dialog that says "Save relative to". You should turn on that check button and choose your density map to get the atom coordinates saved using the coordinate system of the map. I see two possible problems. You didn't check the check-button on the save dialog for the "save relative to" option. In that case it saves the coordinates relative to the molecules own coordinate system which is different from the map coordinate system if you have fit the molecule into the map. Another possibility is that when you later open the density map and molecule but you have other models open already. When Chimera opens a new model it has its coordinate system match the coordinate system of the already opened model having lowest id number. So what can go wrong here is you might have your density map opened (model #2) and some other PDB that you just fit into it (model #1) and then you open the former saved PDB. It's initial coordinate system will be that of model #1 (the already open PDB), instead of the density map (model 2 > 1) which makes it not align correctly with the map. If the newly opened misaligned PDB model is model #3 you could remedy this problem with the command (Favorites / Command-Line) matrixcopy #2 #3 to set the coordinate system of the new PDB model (#3) to be the that of the density map (#2). Tom
Hi Guys,
I'm having what I am sure is a trivial problem. When I save my PDB coordinates, I am asked what the reference is, and choose a density map. But when I read those coordinates back in, they are translated/rotated from where they should be and no longer match the density map. Can you tell me what is the correct procedure for setting the reference?
Thanks
Sam