[Chimera-users] maps handling

Benoît Zuber bzuber at mrc-lmb.cam.ac.uk
Wed Feb 11 11:55:40 PST 2009

Hi Tom,

Thank you very much for all the tips! It sounds very straightforward. I'll
try it tomorrow.


> 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

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