[Chimera-users] rotating maps in chimera

Tom Goddard goddard at cgl.ucsf.edu
Thu Apr 19 10:30:34 PDT 2007

Hi Preethi,

  Here's what caused the misalignment when you opened "subtracted map 
2", let's call that one map 3, into Chimera where the original map 2 and 
reoriented map 1 were already opened.  When you open map 3 Chimera 
needed to give it an initial transformation.  Maps 1 and 2 had different 
transforms.  Chimera chooses the transform of the map with the lowest id 
number (shown in Model Panel, menu entry Favorites / Model Panel).  Map 
1 must have had the lowest id number, so it got the transform of map 1 
instead of the transform of map 2.   Chimera had no way of knowing that 
map 3 was just a  modified version of map 2.

  When you open data in Chimera it assigns an id number to it (shown in 
Model Panel).  The id number is 0 for the first opened data set, then 1 
for the next, ....  In general it assigns the lowest available id number 
when a new data set is opened.  When restoring Chimera sessions maps get 
their original model id numbers in Chimera versions 1.2354 and later, 
but are assigned new model id numbers in older versions.

  Since the data sets with lowest id number determines the transform of 
all newly opened models it is best to think of that data set as defining 
the reference frame.

  You can use the Model Panel / Transform As... button to correct the 
transform of a newly opened model.  In the case you  described you would 
need to transform map 3 as map 2 to fix the misalignment.  This is 
probably easier than editing a session file.


preethi at bu.edu wrote:
> Hi Tom,
> Chris I think had already discussed with you about how we transform 
> the PDB files that were originally fit into a brix map so that it now 
> fits into an MRC file in chimera.
> I am just repeating that here because I came across a problem when I 
> did this.
> I saved a session in chimera where I had rotated a MRC map say map 1 
> w.r.t another MRC map 2 and then used the "fit map into map" feature 
> to align map 1 into map 2.So I saved the session(which would save the 
> transformation matrix) and then used the matrix to move certain PDB 
> files(using "transform as").
> Now I did some zoning and volume erasing on map 2(the unrotated map) 
> and then saved the resulting map and then with another program outside 
> chimera subtracted the zoned out volume from the whole volume of map 2.
> SO when I read in the subtracted file into chimera it is now rotated 
> w.r.t the map 2 instead of being read with the original matrix that 
> was used for map2. I fixed this problem by going into chimera session 
> file and maunally changing the rotation and translation values for 
> this map to match that of map2.
> Also, if I opened chimera afresh and didnt restore the session where I 
> had done all the transformations but just opened map 2 and the 
> subtracted map then it reads them correctly without displacing one map 
> w.r.t the other.
> So I was just wondering why chimera automatically rotates the 
> subsequent MRC files that are read into a session where a 
> transformation was applied to some files only ?
> -Preethi

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