[Chimera-users] maps handling

Benoit Zuber bzuber at mrc-lmb.cam.ac.uk
Wed Feb 11 08:53:08 PST 2009


I want to handle a large number of small density maps (around 1000 maps 
of approx 50x50x50 pixels).
I need to group them (in around 5 groups). Then I need to treat all the 
maps of each group in a certain way. For example, I would like to change 
the level threshold for display, or the display style for every maps in 
a group at once. Also I would like to show or hide all maps of a group 
at once.

The maps are not opened in an order related to their group.

I remember someone recently suggested model 'folders' as a new 
functionality. Has this been incorporated in the latest versions of chimera?
Even if it is the case, It would be too tedious to have to click on each 
individual model to assign it to a group. Similarly a simple command 
passed at the command line wouldn't be very elegant: I would have to 
write each volume number since they are unsorted.

I suppose a python script would be much more appropriate. The script 
would have some functions to do tasks like those described above on each 
members of a group and a function to read group composition from a text 

I looked in chimera's programmer guide for a section on volume handling 
but I couldn't find much material on that. Did I miss it? What approach 
would you recommend? I guess I could use runCommand() but there are 
maybe better ways.
Also the script would have to run in interactive mode. I suppose that 
IDLE would work for that purpose. How should I do that? Open IDLE and 
import my module? Where can you define the paths that chimera uses to 
look for packages?

Thanks in advance!

Benoît Zuber
MRC Laboratory of Molecular Biology
Hills Road
United Kingdom
+44 1223 402209
bzuber at mrc-lmb.cam.ac.uk

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