Encode: saving a movie on a Windows laptop, and colouring residues in the multiple sequence
Dear ChimeraX My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please? Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV. Thank you, 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
Hi Anne-Frances, I'm not a Windows user (and don't have one handy to test) but on your Windows laptop you could try clicking the the movie-camera icon on the toolbar across the top, Home tab, and see whether if gives a suitable location and format on that platform. The command(s) it uses will be shown in the Log. Then you can suggest something similar to your students (at least in terms of the location and file format). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home> Sorry, to my knowledge there aren't currently any options for different coloring of the amino acid codes in the sequence alignment window. The Settings of the ChimeraX Sequence Viewer have an Appearance section but currently it just covers spacing and wrapping. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings> I hope this helps, 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 30, 2025, at 11:56 AM, Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX
My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please?
Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV.
Thank you, Anne-Frances
On Jan 30, 2025, at 12:18 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Sorry, to my knowledge there aren't currently any options for different coloring of the amino acid codes in the sequence alignment window.
Hi Anne-Frances, We do have a ticket open for this capability (#15475 (Unable to synchronize structure colouring with sequence colouring) <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15475#no3>). I’ve added you to the recipient list for the ticket. --Eric Eric Pettersen UCSF Computer Graphics Lab
Thank you very much Eric, This will be great to have. 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 30, 2025, at 16:51, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
On Jan 30, 2025, at 12:18 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Sorry, to my knowledge there aren't currently any options for different coloring of the amino acid codes in the sequence alignment window.
Hi Anne-Frances, We do have a ticket open for this capability (#15475 (Unable to synchronize structure colouring with sequence colouring) <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15475#no3>). I’ve added you to the recipient list for the ticket.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Thank you very much for a real-time response Elaine, Eric has also answered re. the sequence colouring. I will share your very good tip with the class for all users making movies. 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 30, 2025, at 15:18, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Anne-Frances, I'm not a Windows user (and don't have one handy to test) but on your Windows laptop you could try clicking the the movie-camera icon on the toolbar across the top, Home tab, and see whether if gives a suitable location and format on that platform. The command(s) it uses will be shown in the Log. Then you can suggest something similar to your students (at least in terms of the location and file format).
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html#home>
Sorry, to my knowledge there aren't currently any options for different coloring of the amino acid codes in the sequence alignment window.
The Settings of the ChimeraX Sequence Viewer have an Appearance section but currently it just covers spacing and wrapping.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings>
I hope this helps, 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 30, 2025, at 11:56 AM, Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX
My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please?
Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV.
Thank you, Anne-Frances
participants (3)
-
Anne-Frances Miller -
Elaine Meng -
Eric Pettersen