Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford
Hi Luiza, This page lists the file types Chimera can read: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> Searching for "IMOD" in the above, I see IMOD map format (.rec) and IMOD segmentation meshes (.imod, .mod) and link to more detailed information about the latter in another page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod.html> That second link says only mesh data are read from the IMOD segmentation, not the contour data. However, it also explains how to make a small change to the code to also read the contours. I hope this helps Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2020, at 3:33 AM, Luiza Mendonça <luiza@strubi.ox.ac.uk> wrote:
Good morning,
Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help.
Best, Luiza Mendonca Zhang Lab University of Oxford
Hi Luiza, Our newer program ChimeraX can read points from imod files. You have to open it with the "contours true" option, for example, open ~/Desktop/particles.imod contours true Documentation https://www.rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html I just tested it and it gave an error. I fixed the code so tonight's ChimeraX build will be able to read IMOD points and contour lines. The daily builds are below the releases on the download page https://www.rbvi.ucsf.edu/chimerax/download.html#daily Tom
On Dec 12, 2020, at 3:33 AM, Luiza Mendonça <luiza@strubi.ox.ac.uk> wrote:
Good morning,
Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help.
Best, Luiza Mendonca Zhang Lab University of Oxford _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Elaine and Tom, Elaine, even after changing the .py and restarting chimera, the model points won't open... But thank you for the help anyway. Tom, I will wait for tomorrow to download ChimeraX, thanks! Best, Luiza On Sat, 12 Dec 2020 at 19:11, Tom Goddard <goddard@sonic.net> wrote:
Hi Luiza,
Our newer program ChimeraX can read points from imod files. You have to open it with the "contours true" option, for example,
open ~/Desktop/particles.imod contours true
Documentation
https://www.rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html
I just tested it and it gave an error. I fixed the code so tonight's ChimeraX build will be able to read IMOD points and contour lines. The daily builds are below the releases on the download page
https://www.rbvi.ucsf.edu/chimerax/download.html#daily
Tom
On Dec 12, 2020, at 3:33 AM, Luiza Mendonça <luiza@strubi.ox.ac.uk> wrote:
Good morning,
Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help.
Best, Luiza Mendonca Zhang Lab University of Oxford _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Luiza Mendonça -
Tom Goddard