Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood
Dear ChimeraX I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file. I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary. I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html> I was curious if anyone has had experience with cubefiles. Any assistance would be greatly appreciated, Very Respectfully, Nathan Wood
Hi Nathan, The previous posts aren't that relevant... April 2021 doesn't apply unless your cube file contains atomic coordinates that you are trying to view. The relevant part of the May 2020 post is: "If you open a .cube file it will automatically show as isosurfaces." You could still use the Volume Viewer interface after that to adjust the isosurface levels and their colors, of course. Don't know what you mean by "from the shell" or "difficulties" or "incompletely visualize" though. You can first start ChimeraX and then use its File... Open menu, or the "open" command, e.g. "open browse" if you want to use a file browser interface to locate your cube file. Make sure you are using a reasonably new ChimeraX, e.g. the latest production release. If that doesn't show isosurfaces, I couldn't say anything else unless you provide the cube file itself and probably also give more details about what exactly is problematic. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2021, at 7:43 PM, Nathan Wood via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX
I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file.
I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary.
I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html>
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html>
I was curious if anyone has had experience with cubefiles.
Any assistance would be greatly appreciated,
Very Respectfully,
Nathan Wood
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dr. Elaine Meng, Unfortunately I was rather negligent and I do not think I ever replied to you. 1. I was able to resolve my issues with the Volume Viewer, when I had mentioned 'from the shell' I had originally meant the command line provided within the ChimeraX GUI 2. I have encountered another issue with regards to using the API call label(session,...) as imported through 'from chimerax.label import label3d'. I intend to write a script that can label values to specific atoms and I am not sure how to move forward with the issues mentioned below. - When I attempt to run `label(session,...)`I would return the error "NameError: name 'label' is not defined" - Furthermore, when I attempt to instead run 'label3d(session,...)` I return an error that " the module is not callable" Any assistance would be appreciated and more information can be provided. Very Respectfully, Nathan Wood On 7/13/21 11:58 AM, Elaine Meng wrote:
[External Email]
Hi Nathan, The previous posts aren't that relevant... April 2021 doesn't apply unless your cube file contains atomic coordinates that you are trying to view. The relevant part of the May 2020 post is: "If you open a .cube file it will automatically show as isosurfaces."
You could still use the Volume Viewer interface after that to adjust the isosurface levels and their colors, of course.
Don't know what you mean by "from the shell" or "difficulties" or "incompletely visualize" though. You can first start ChimeraX and then use its File... Open menu, or the "open" command, e.g. "open browse" if you want to use a file browser interface to locate your cube file. Make sure you are using a reasonably new ChimeraX, e.g. the latest production release.
If that doesn't show isosurfaces, I couldn't say anything else unless you provide the cube file itself and probably also give more details about what exactly is problematic. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2021, at 7:43 PM, Nathan Wood via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX
I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file.
I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary.
I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing.
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2021-2DApril_002126.html&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=KFA7ieP_G7kuCfY0NgzQOQ&m=DNgoVyjxQTakdijZJGdkYJnKnaR20gQF4ZM_Vk4vmYA&s=mPtugH4dUvVyGFhC3jIuAMtBtKOG2ygUWzWSEAmjpao&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2021-2DApril_002126.html&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=KFA7ieP_G7kuCfY0NgzQOQ&m=DNgoVyjxQTakdijZJGdkYJnKnaR20gQF4ZM_Vk4vmYA&s=mPtugH4dUvVyGFhC3jIuAMtBtKOG2ygUWzWSEAmjpao&e= >
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2020-2DMay_001110.html&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=KFA7ieP_G7kuCfY0NgzQOQ&m=DNgoVyjxQTakdijZJGdkYJnKnaR20gQF4ZM_Vk4vmYA&s=5OapB-hdINjPQRouMatA4gKvoh8mqn-ETMjzKIAhfdc&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_pipermail_chimerax-2Dusers_2020-2DMay_001110.html&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=KFA7ieP_G7kuCfY0NgzQOQ&m=DNgoVyjxQTakdijZJGdkYJnKnaR20gQF4ZM_Vk4vmYA&s=5OapB-hdINjPQRouMatA4gKvoh8mqn-ETMjzKIAhfdc&e= >
I was curious if anyone has had experience with cubefiles.
Any assistance would be greatly appreciated,
Very Respectfully,
Nathan Wood
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=KFA7ieP_G7kuCfY0NgzQOQ&m=DNgoVyjxQTakdijZJGdkYJnKnaR20gQF4ZM_Vk4vmYA&s=YTwQ5B7gTKak4gwe9C6TVALESqHa_-FwRb78IefPnEk&e=
Hi Nathan, I'm not sure why you're resorting to the Python layer to do this. AFAIK, the "label" command's text option can label atoms with arbitrary text, including values from that atom's attributes. Perhaps you do need to provide more information about why that doesn't work for you. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 8, 2021, at 7:43 PM, Nathan Wood via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
2. I have encountered another issue with regards to using the API call label(session,...) as imported through 'from chimerax.label import label3d'. I intend to write a script that can label values to specific atoms and I am not sure how to move forward with the issues mentioned below.
- When I attempt to run `label(session,...)`I would return the error "NameError: name 'label' is not defined"
- Furthermore, when I attempt to instead run 'label3d(session,...)` I return an error that " the module is not callable"
Any assistance would be appreciated and more information can be provided.
participants (3)
-
Elaine Meng -
Eric Pettersen -
Nathan Wood