<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">There is a ChimeraX feature request for having the CUBE file reader show both the map and the atomic model.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4207</a></div><div class=""><br class=""></div><div class="">I am not sure when that will get done, so for now the ChimeraX recipes script can be used.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 9, 2021, at 6:07 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Carles,<br class="">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:<br class=""><br class="">(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.<br class=""><<a href="https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html" class="">https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html</a>><br class=""><br class="">(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.<br class=""><br class="">(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"). <br class=""><br class="">**I will send you the resulting PDB file in a separate message in case it is private data.**<br class=""><br class="">(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:<br class=""><br class="">open carles-atomic.pdb coordsets true<br class=""><br class="">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.<br class=""><br class="">When the bug is fixed (#4487 <<a href="https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487" class="">https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487</a>>), step #3 would not be necessary.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Apr 7, 2021, at 9:33 AM, Anthony James Schaefer <<a href="mailto:tony.schaefer@uga.edu" class="">tony.schaefer@uga.edu</a>> wrote:<br class=""><br class="">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: <a href="https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html" class="">https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html</a><br class=""><br class=""><blockquote type="cite" class=""><br class=""><blockquote type="cite" class="">On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <<a href="mailto:carles.serrat-jurado@upc.edu" class="">carles.serrat-jurado@upc.edu</a>> wrote:<br class=""><br class="">Dear Elaine,<br class=""><br class="">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.<br class=""><br class="">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.<br class=""><br class="">Thank you very much in advance for your support.<br class=""><br class="">Best regards,<br class=""><br class="">Carles<br class=""><br class=""><ChimeraX.png><br class=""><br class=""><VESTA.png><br class=""><cube_files.zip><br class="">—————————-—————————<br class="">Prof. Carles Serrat (PhD)<br class="">Department of Physics<br class="">UPC - Polytechnic University of Catalonia<br class="">Colom 11, 08222 - Terrassa<br class="">Phone: +34 93 739 8137<br class="">Mobile: +34 696 738 728<br class=""><a href="https://donll.upc.edu" class="">https://donll.upc.edu</a><br class="">——————————————————-<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class="">ChimeraX-users@cgl.ucsf.edu<br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>