[Chimera-users] maps handling

Tom Goddard goddard at cgl.ucsf.edu
Wed Feb 11 09:09:31 PST 2009

Hi Ben,

  You can make these groupings with the alias command and operate on all 
maps in a group with the volume command.  Here's an example setting the 
contour level of 5 maps and mesh display style.

    alias g1 #1,2,17,25,33
    volume g1 level 0.5 style mesh

You will probably want to ut the alias commands giving the model id 
numbers of the 5 groups in a command file (.cmd suffix) and then just 
open that file in Chimera (e.g. "open galiases.cmd").

  Here's documentation for the commands.



  Model "folders" have not been implemented.

  The programmer's guide has little useful information except for the 
examples section.  The rest is auto-generated from scant code comments.  
There is not a volume example, though there have been many volume 
scripts posted to the mailing list.  Can't think of any easy way to find 
those though -- maybe search the archives for the word python.  I intend 
to make a web page of Chimera scripts some day.  The usual method of 
running Python scripts in Chimera is to write them in a text editor to a 
file and open that file in Chimera with File / Open or the open command.


Benoit Zuber wrote:
> Hi,
> 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 
> file.
> 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!
> Ben

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