Thank you. My script now works on my workstation. On another linux machine where I am running the headless chimera, it is not processed. I start it with chimera —send tmp.py but all I end up in is the chimera console. Any suggestions? Thanks, Thomas On Dec 30, 2013, at 12:05 PM, Tom Goddard <goddard@sonic.net> wrote:

Hi Thomas,

You need

mod.show()

to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code

mod.surface_levels = [-1,0]

is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use

mod.surface_levels = [-1]

Tom

On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote:

...

Hi everyone,

I have this line of code where I want to load a density and export a negative surface of it:

import chimera as ch mod = ch.openModels.open(‘./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html’)

However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels?

Thanks, Thomas

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Chimera command-line flags described here http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html Tom On Dec 30, 2013, at 12:48 PM, Tom Goddard wrote:

Hi Thomas,

I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug… in Chimera (non-headless version) and explain that the problem is with the linux headless version.

Tom

On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote:

...

Thank you.

My script now works on my workstation. On another linux machine where I am running the headless chimera, it is not processed.

I start it with

chimera —send tmp.py

but all I end up in is the chimera console.

Any suggestions? Thanks, Thomas

On Dec 30, 2013, at 12:05 PM, Tom Goddard <goddard@sonic.net> wrote:

...

Hi Thomas,

You need

mod.show()

to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code

mod.surface_levels = [-1,0]

is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use

mod.surface_levels = [-1]

Tom

On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote:

...

Hi everyone,

I have this line of code where I want to load a density and export a negative surface of it:

import chimera as ch mod = ch.openModels.open(‘./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html’)

However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels?

Thanks, Thomas

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Thomas, The best way to set the contour level and also to turn off capping box faces is by calling the set_parameters() method. mod.set_parameters(surface_levels = [-1], cap_faces = False) mod.show() Tom On Dec 30, 2013, at 1:32 PM, Thomas Hrabe wrote:

Thank you Tom,

the script parameter was what I was looking for. My headless chimera now exports those webgl html files.

One more question: if I display negative density, how do I programmatically set Surface & Mesh options > Cap high values at box faces?

Thanks, Thomas

On Dec 30, 2013, at 12:48 PM, Tom Goddard <goddard@sonic.net> wrote:

...

Hi Thomas,

I'm not sure why "chimera --send tmp.py" is not working. But I am also confused why you are using the "--send" option? That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running). If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments. If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug… in Chimera (non-headless version) and explain that the problem is with the linux headless version.

Tom

On Dec 30, 2013, at 12:40 PM, Thomas Hrabe wrote:

...

Thank you.

My script now works on my workstation. On another linux machine where I am running the headless chimera, it is not processed.

I start it with

chimera —send tmp.py

but all I end up in is the chimera console.

Any suggestions? Thanks, Thomas

On Dec 30, 2013, at 12:05 PM, Tom Goddard <goddard@sonic.net> wrote:

...

Hi Thomas,

You need

mod.show()

to have the density map recompute its contour surface. You can remove the mod.display = True line. Your code

mod.surface_levels = [-1,0]

is setting two contour levels one at density value -1 and one at 0. Is that what you intend? If you only wanted a single level you would use

mod.surface_levels = [-1]

Tom

On Dec 27, 2013, at 3:24 PM, Thomas Hrabe wrote:

...

Hi everyone,

I have this line of code where I want to load a density and export a negative surface of it:

import chimera as ch mod = ch.openModels.open(‘./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html’)

However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels?

Thanks, Thomas

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users