[Chimera-users] reference for saving pdb

Tom Goddard goddard at cgl.ucsf.edu
Fri Feb 12 18:04:14 PST 2010

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).


> 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

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