Hello,
I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time.
Best,
Lauren Lehmann
Biochemistry Graduate Student University of Oregon
Hello Lauren, This is a partial answer: you could consider ChimeraX command scripts or python scripts.
For ChimeraX command scripts at least, there is complete documentation of syntax and options for nearly every command:
http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html#commands
Also, there are several tutorials with commands shown, and most of the “feature highlights” and “example images” on the ChimeraX website link to the respective .cxc files (ChimeraX command files) used to set up the images.
http://www.rbvi.ucsf.edu/chimerax/tutorials.html http://www.rbvi.ucsf.edu/chimerax/features.html http://www.rbvi.ucsf.edu/chimerax/gallery.html
Further, using many of the GUIs or icons to perform actions shows the corresponding command in the Log to facilitate learning the commands. As time goes by we will have more examples, more highlights, and more tutorials.
On the python side, I know we plan to have APIs available, but as resources are limited I can’t give much details or a timeline.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 21, 2020, at 12:39 PM, llehmann@uoregon.edu wrote:
Hello,
I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time.
Best,
Lauren Lehmann
Biochemistry Graduate Student University of Oregon _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Lauren, If you outlined the missing features you would need, we could provide some idea if those features will become available soon or… not soon.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 21, 2020, at 12:39 PM, llehmann@uoregon.edu wrote:
Hello,
I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time.
Best,
Lauren Lehmann
Biochemistry Graduate Student University of Oregon _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Eric,
Thank you for your reply! We're generally looking for a script library/repository similar to what PyMOL's wiki has (https://pymolwiki.org/index.php/Category:Script_Library). Some scripts we use already have a command in ChimeraX with the same functionality. An example of a script we use in PyMOL would be BbPlane, however we're more interested in script libraries as a general resource rather than replacing exact scripts, as we use so many different scripts in the course. Like I said, I understand that ChimeraX is still in early stages so we're more looking to get a sense of whether this kind of feature will ever exist.
Best, Lauren Lehmann Biochemistry Graduate Student University of Oregon
On 2020-01-22 11:41 am, Eric Pettersen wrote:
Hi Lauren, If you outlined the missing features you would need, we could provide some idea if those features will become available soon or… not soon.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 21, 2020, at 12:39 PM, llehmann@uoregon.edu wrote:
Hello,
I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time.
Best,
Lauren Lehmann
Biochemistry Graduate Student University of Oregon _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users [1]
Links:
[1] https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/mailman/listinfo/chimer...
In the long term we do intend to have something along those lines in lieu of the simple “Python scripts page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts” that we have for Chimera. It may be awhile though. We also have to work out how to allow relevant people to edit it without allowing everyone on the internet to edit it…
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 22, 2020, at 12:30 PM, llehmann@uoregon.edu wrote:
Hi Eric,
Thank you for your reply! We're generally looking for a script library/repository similar to what PyMOL's wiki has (https://pymolwiki.org/index.php/Category:Script_Library https://pymolwiki.org/index.php/Category:Script_Library). Some scripts we use already have a command in ChimeraX with the same functionality. An example of a script we use in PyMOL would be BbPlane, however we're more interested in script libraries as a general resource rather than replacing exact scripts, as we use so many different scripts in the course. Like I said, I understand that ChimeraX is still in early stages so we're more looking to get a sense of whether this kind of feature will ever exist.
Best, Lauren Lehmann Biochemistry Graduate Student University of Oregon
On 2020-01-22 11:41 am, Eric Pettersen wrote:
Hi Lauren, If you outlined the missing features you would need, we could provide some idea if those features will become available soon or… not soon. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 21, 2020, at 12:39 PM, llehmann@uoregon.edu wrote: Hello, I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time. Best, Lauren Lehmann Biochemistry Graduate Student University of Oregon _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users [1]
Links:
[1] https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/mailman/listinfo/chimer... https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!C5qS4YX3!QfY8fpfCg1qDjE7VnNB3WFxm17lX1r8hQcmbEm3_gMtJcmjRz3YSdM8BPvc_Cq8Vzg$
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participants (3)
-
Elaine Meng -
Eric Pettersen -
llehmann＠uoregon.edu