Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Oh shoot! You are right,
I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced.
Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow.
This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf
THANK YOU for answering on a Sunday!! Anne-Frances
Hi, This is by no means an official tutorial but if it's of any help, here is a "getting started" ChimeraX tutorial that I prepared for our Structural Biology block course last September: https://docs.google.com/document/d/15v0dm-J0kwD6oTIsQ2R06c393cfJJe9bh7EM0HY9... It covers the basics of operations on protein sequences and structures, rendering surface attributes, assessing quality of predicted structures and scripting. Feel free to reuse and remix with attribution to the source. -- Ricardo Diogo Righetto Em seg., 13 de jan. de 2025 às 18:40, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> escreveu:
Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera.
However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is
Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html
You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials.
You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them).
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Oh shoot! You are right,
I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced.
Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow.
This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf
THANK YOU for answering on a Sunday!! Anne-Frances
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you both very much! I remain stunnedm grateful and amazed that Elaine answered on a Sunday evening!!! Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/ Visiting Fellow, Einstein Foundation of Berlin
On Jan 13, 2025, at 13:39, Ricardo Righetto <ricardorighetto@gmail.com> wrote:
Hi,
This is by no means an official tutorial but if it's of any help, here is a "getting started" ChimeraX tutorial that I prepared for our Structural Biology block course last September: https://docs.google.com/document/d/15v0dm-J0kwD6oTIsQ2R06c393cfJJe9bh7EM0HY9... It covers the basics of operations on protein sequences and structures, rendering surface attributes, assessing quality of predicted structures and scripting.
Feel free to reuse and remix with attribution to the source.
-- Ricardo Diogo Righetto
Em seg., 13 de jan. de 2025 às 18:40, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> escreveu:
Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera.
However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is
Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>
You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials.
You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them).
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2@gmail.com <mailto:afmill3r2@gmail.com>> wrote:
Oh shoot! You are right,
I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced.
Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow.
This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf
THANK YOU for answering on a Sunday!! Anne-Frances
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks Ricardo, that looks great!! Elaine
On Jan 13, 2025, at 10:39 AM, Ricardo Righetto <ricardorighetto@gmail.com> wrote:
Hi,
This is by no means an official tutorial but if it's of any help, here is a "getting started" ChimeraX tutorial that I prepared for our Structural Biology block course last September: https://docs.google.com/document/d/15v0dm-J0kwD6oTIsQ2R06c393cfJJe9bh7EM0HY9... It covers the basics of operations on protein sequences and structures, rendering surface attributes, assessing quality of predicted structures and scripting.
Feel free to reuse and remix with attribution to the source.
-- Ricardo Diogo Righetto
Em seg., 13 de jan. de 2025 às 18:40, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escreveu: Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera.
However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is
Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html>
You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials.
You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them).
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2@gmail.com> wrote:
Oh shoot! You are right,
I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced.
Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow.
This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf
THANK YOU for answering on a Sunday!! Anne-Frances
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Anne-Frances Miller -
Elaine Meng -
Ricardo Righetto