[Chimera-users] maps handling

[Tom Goddard]

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.

    http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html

    http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html

  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.

    Tom


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
>
>