ChimeraX reading cube files
Hi Carles, We recommend using the chimerax-users@cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private. ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format. This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
Hi Carles, I'm no Gaussian expert, but the SEQCROW tool can read Gaussian log files, which might help. You can download SEQCROW from the ChimeraX Toolshed, which you can access via Tools→More Tools... in ChimeraX. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2021, at 8:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Carles, We recommend using the chimerax-users@cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private.
ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format.
This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, April 7, 2021 12:21 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Carles Serrat Jurado <carles.serrat-jurado@upc.edu> Subject: Re: [chimerax-users] ChimeraX reading cube files [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Carles, I'm no Gaussian expert, but the SEQCROW tool can read Gaussian log files, which might help. You can download SEQCROW from the ChimeraX Toolshed, which you can access via Tools→More Tools... in ChimeraX. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2021, at 8:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Carles, We recommend using the chimerax-users@cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private.
ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format.
This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
Dear Carles, It took me a couple of days to try that recipe script on your data, sorry about the slow reply. Now I realize there are a few extra steps to convert your data to a trajectory (e.g. with slider to play as movie), so I thought I should share the details with the list: (1) In ChimeraX, I opened your 10 cube files, and then I used the python file in the ChimeraX recipe to create 10 atomic models. <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html> (2) Then I saved the 10 atomic models as a single PDB file (using ChimeraX menu: File... Save), File type PDB, relative to the first atomic model. Doesn't matter which one you choose as the "relative to" model, however. (3) Then I was going to open that single PDB file as a trajectory. However, there is a bug in the saving that currently prevents it. The bug puts "END" after each atomic structure in the file. So I first needed to text-edit the PDB file to remove all of the "END" lines (but not "ENDMDL"). **I will send you the resulting PDB file in a separate message in case it is private data.** (4) In ChimeraX, I closed all the other models and then opened the new edited multi-model PDB file with the "coordsets" option to make it into a trajectory, for example, command: open carles-atomic.pdb coordsets true However, 10 frames of the trajectory all look exactly the same to me, but far as I know that is a correct conversion of the data from the 10 cube files you sent me. When the bug is fixed (#4487 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487>), step #3 would not be necessary. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 9:33 AM, Anthony James Schaefer <tony.schaefer@uga.edu> wrote:
ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
There is a ChimeraX feature request for having the CUBE file reader show both the map and the atomic model. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207> I am not sure when that will get done, so for now the ChimeraX recipes script can be used. Tom
On Apr 9, 2021, at 6:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Carles, It took me a couple of days to try that recipe script on your data, sorry about the slow reply. Now I realize there are a few extra steps to convert your data to a trajectory (e.g. with slider to play as movie), so I thought I should share the details with the list:
(1) In ChimeraX, I opened your 10 cube files, and then I used the python file in the ChimeraX recipe to create 10 atomic models. <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html>
(2) Then I saved the 10 atomic models as a single PDB file (using ChimeraX menu: File... Save), File type PDB, relative to the first atomic model. Doesn't matter which one you choose as the "relative to" model, however.
(3) Then I was going to open that single PDB file as a trajectory. However, there is a bug in the saving that currently prevents it. The bug puts "END" after each atomic structure in the file. So I first needed to text-edit the PDB file to remove all of the "END" lines (but not "ENDMDL").
**I will send you the resulting PDB file in a separate message in case it is private data.**
(4) In ChimeraX, I closed all the other models and then opened the new edited multi-model PDB file with the "coordsets" option to make it into a trajectory, for example, command:
open carles-atomic.pdb coordsets true
However, 10 frames of the trajectory all look exactly the same to me, but far as I know that is a correct conversion of the data from the 10 cube files you sent me.
When the bug is fixed (#4487 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487>), step #3 would not be necessary.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 9:33 AM, Anthony James Schaefer <tony.schaefer@uga.edu> wrote:
ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks a lot, Elaine, Eric and Anthony! Carles
On Apr 7, 2021, at 6:21 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Carles, I'm no Gaussian expert, but the SEQCROW tool can read Gaussian log files, which might help. You can download SEQCROW from the ChimeraX Toolshed, which you can access via Tools→More Tools... in ChimeraX.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2021, at 8:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Carles, We recommend using the chimerax-users@cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private.
ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format.
This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado@upc.edu> wrote:
Dear Elaine,
I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA.
My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on.
Thank you very much in advance for your support.
Best regards,
Carles
<ChimeraX.png>
<VESTA.png> <cube_files.zip> —————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
—————————-————————— Prof. Carles Serrat (PhD) Department of Physics UPC - Polytechnic University of Catalonia Colom 11, 08222 - Terrassa Phone: +34 93 739 8137 Mobile: +34 696 738 728 https://donll.upc.edu ——————————————————-
participants (5)
-
Anthony James Schaefer -
Carles Serrat Jurado -
Elaine Meng -
Eric Pettersen -
Tom Goddard