Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da
Hi Daniel, Are you just using the open dialog from the File menu? There is an "open" command "vseries" option for designating multiple maps as a volume series when they would not be automatically recognized as such.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#vseries http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries
Certainly you can use "open" to open maps and "save" to save them in a different format, if that is still desired.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map
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 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop. Best, -da
Hi Daniel, 'vseries' is broken right now with anything other than .cmap files. I'll send more mail when I have further news.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I mean "open ... vseries true". The "vseries" command itself works fine.
--Eric
On Jul 15, 2020, at 3:40 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Daniel, 'vseries' is broken right now with anything other than .cmap files. I'll send more mail when I have further news.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da _______________________________________________ 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
Okay, fixing it was pretty simple. Tomorrow's daily build will have the fix.
--Eric
On Jul 15, 2020, at 3:40 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Daniel, 'vseries' is broken right now with anything other than .cmap files. I'll send more mail when I have further news.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da _______________________________________________ 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 all, it works very nicely now. (And no display, remote cmaps are still convenient for the old laptop).
Best, -da
On Wed, Jul 15, 2020 at 3:57 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
Okay, fixing it was pretty simple. Tomorrow's daily build will have the fix.
--Eric
On Jul 15, 2020, at 3:40 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Daniel, 'vseries' is broken right now with anything other than .cmap
files. I'll send more mail when I have further news.
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Jul 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu
wrote:
Hi all, I have only been able to load volume series data using the .cmap format
(using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da _______________________________________________ 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
Hi Daniel,
In theory you should be open your MRC files as a series with ChimeraX command "open map*.mrc vseries true". But the vseries option is currently broken as described in bug report
https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3519#comment:7 https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3519#comment:7
Probably Eric will fix that in a day or two.
If you still prefer making the cmap file, ChimeraX is the only thing that writes those files, cmap stands for Chimera map, and I think you could run chimerax like "chimerax --nogui --exit --cmd "open maps*.mrc ; save map.cmap models #1-100" using the "--cmd" option described in the docs
https://www.rbvi.ucsf.edu/chimerax/docs/user/options.html https://www.rbvi.ucsf.edu/chimerax/docs/user/options.html
to run a command (here two commands separated by semicolon) instead of starting the ChimeraX GUI. Worked when I tried it. The "100" can be larger than the number of models without causing any errors so you don't need to know exactly how many maps you are saving.
Tom
On Jul 15, 2020, at 12:14 PM, Daniel Asarnow asarnow@msg.ucsf.edu wrote:
Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop.
Best, -da _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Daniel Asarnow -
Elaine Meng -
Eric Pettersen -
Tom Goddard