[Chimera-users] reference for saving pdb
goddard at cgl.ucsf.edu
Fri Feb 12 18:04:14 PST 2010
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).
> 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?
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