[Chimera-users] Script parameters

[Will Moore]

Hi Tom,

  Thanks for that. Works great!

Now I have another question:

I'm trying to pass colors to the script in the arguments, but not  
having much luck.
In the script itself, do you recover the arguments in the normal way:
Like this?

import getopt, sys, os
try:
	opts, args = getopt.getopt(sys.argv[1:] ,"a:", [])
except getopt.GetoptError, err:
	pass
returnMap = {}
print opts
for opt, arg in opts:
	if opt == "-a":
		returnMap["a"] = arg	
print returnMap


If I run this script directly from the command line like this:
python colourMaps.py -a red

I get the expected print out
[('-a', 'red')]
{'a': 'red'}

but if I try to call this script at the same time as opening maps from  
the command line, I don't get anything:
chimera volume.mrc --script colourMaps.py -- -a red

Reply log:
[]
{}

I'm also getting a UI dialog
"Please designate file type for --script"
which I have to 'cancel' every time I open chimera with this command.
Is there any way I can avoid this?

  Many thanks,


   Will.


On 15 Mar 2010, at 17:25, Thomas Goddard wrote:

> Hi Will,
>
>  Here's a Python script that will change a volume color:
>
> from chimera import openModels
> from VolumeViewer import Volume
> for v in openModels.list(modelTypes=[Volume]):
>    v.set_parameters(surface_colors = [(1.0, 0.0, 0.0, 1.0)])
>    v.show()
>
> You can do the same thing more easily with a Chimera command and you  
> can put such commands in a file (suffix .cmd) for Chimera to execute  
> (by opening the file).
>
> 	volume # color plum
>
> This colors all volume models as plum color.  If you wanted a  
> specific model you would use for example #2 instead of #.  The  
> notation # means all models.
>
> You could also run this Chimera command from Python.
>
> from chimera import runCommand
> runCommand("volume # color plum")
>
>
> 	Tom
>
>
>
>> Hi,
>>
>> I'm trying to write a script to change the surface colors of  
>> volumes in
>> Chimera:
>>
>> This is what I have so far.
>>
>> for m in chimera.openModels.list():
>> print m.surface_colors
>> m.surface_colors = [(1.0, 0.0, 0.0, 1.0)]
>> print m.surface_colors
>>
>> This seems to alter the surface colors, but has no effect on what the
>> maps look like in the UI.
>> Do I need to call something else for the UI to be updated, or am I  
>> using
>> the wrong approach entirely?
>>
>> Also, I would like to only select the volumes in the first line but I
>> don't know what modelTypes this is:
>> for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
>>
>> Many thanks,
>>
>> Will.
>>
>>
>>
>> William Moore
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee DD1 5EH
>> United Kingdom
>>
>> Phone 01382 386364
>> http://openmicroscopy.org.uk
>>

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org.uk