[Chimera-users] comparing maps with different orientations

Cathy Lawson cathy.lawson at rutgers.edu
Mon Oct 3 11:28:22 PDT 2016


Thanks Tom,
I knew you’d have a good suggestion — I’ll try it out!
Cathy

> On Oct 3, 2016, at 2:02 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Cathy,
> 
>   I think you should use the fit atomic structure to do the alignment.  Here’s how.  Open a copy of the atomic structure in and put it in the orientation you want for the maps, I’ll call this the reference structure (#0).  Now open your first map (#1) with its fit structure (#2).  Align the fit atomic structure with the reference atomic structure
> 
> 	match #2 #0
> 
> Then move the map so it aligns with its fit atomic structure.
> 
> 	matrixcopy #2 #1
> 
> The reference structure need not be displayed to do this.  Now save an image
> 
> 	copy some/directory/map1.png supersample 3
> 
> Then close the first map and model and load the second map and model and repeat.
> 
> 	close #1,2
> 
> You could make a command script that has repetitions of these command plus two open commands before the map to open the map and fit model, and then run that script in Chimera (just use File / Open, and script file with suffix *.cmd), and that will produce all the images.  You might want to save the reference model in the desired orientation as a Chimera session file so you can rerun with exactly the same orientation at a later date if you decide to change something (e.g. image size, background color).
> 
>   Tom
> 
> 
>> On Oct 3, 2016, at 7:58 AM, Cathy Lawson  wrote:
>> 
>> Dear USCF Chimera Team,
>> 
>> I’m looking for suggestions on how to go about the following:
>> For the EMDataBank map challenge we have sets of EM maps of the same molecule that have been submitted in different orientations.
>> We’d like to automate production of images for each set of maps with a common orientation/scale so that they can be readily compared.
>> Models fitted to each map are in principle available, so this could be part the process if needed (e.g., to define transformations between map positions/orientations).
>> 
>> Many thanks,
>> 
>> Cathy
>> 
>> 
>> 
>> ******************
>> Catherine Lawson, Ph.D.
>> EMDataBank, RCSB PDB
>> Center for Integrative Proteomics Research
>> Rutgers University
>> http://emdatabank.org <http://emdatabank.org/>
>> 
>> 
>> 
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>> 
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