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From: Allen Place <place@umces.edu> Subject: Re: Your message to chimerax-users@cgl.ucsf.edu awaits moderator approval Date: May 16, 2024 at 5:11:31 AM PDT To: chimerax-users-bounces@cgl.ucsf.edu
Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. Al
On May 15, 2024, at 9:45 AM, chimerax-users-bounces@cgl.ucsf.edu wrote:
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Alphafold3 models
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Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful”
He is smart, makes friends easily, and never loses his sense of humour.
He thrives on a challenge

Sign up to receive our quarterly newsletter, Inside IMET!
Hi Al, I'm not sure if you mean you want to recolor the boxes on the sequence, or the corresponding parts of the 3D structure (if any) in the main graphics window. (A) For the 3D structure: If you have a 3D structure associated with the sequence, then clicking the sequence region also automatically selects that part of the structure. The selected parts will be outlined with green in the main graphics window. If you don't know what I mean by "associated with" see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...> You can use the Actions menu (e.g. Actions... Color... etc.) to act on your current selection in the 3D structure. Using the Actions menu generates the corresponding command and shows it in the Log, which is meant to help people learn the corresponding commands and also allow scripting these actions. Or, instead of using the menu, you could just enter the command directly. Generally to color the current selection regardless of how that selection was made, you would use the "color" command with "sel" to mean the current selection, e.g. color sel hot pink target ar "target ar" means color both the ribbons and atoms, "target r" would mean ribbons only, "target a" atoms only, etc. They may not be displayed at the time. To actually show the atoms you could again use the Actions menu (Actions... Atoms/Bonds... Show) or just use the corresponding command, e.g. show sel There is also undo/redo if you mess up and want to go back, via "undo" and "redo" commands or Edit menu. There are help pages for all of these commands explaining their options. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> (B) To recolor the boxes on the sequence, the GUI (rather than commands) is the way to go. If you are using the UniProt sequence features dialog, click the color squares to open the system color editor and edit the color interactively. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot> If you are not using the UniProt sequence features dialog, you can use the sequence window context menu Annotations... Regions... (show a context menu by right-click, or if Mac Ctrl-click on the tool, in this case the sequence window) to open the Region Browser, which also has color wells for changing the box interior and border colors. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regionbro...> 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
From: Allen Place <place@umces.edu> Date: May 16, 2024 at 5:11:31 AM PDT
Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. Al
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
Also it is not necessary to go through selection; if you're just going to use a command and you already know the structure residue number range(s) that you want, you can specify them directly in the command, for example: color /A:48-66,125-138 orange How to specify models, chains, residues, atoms in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine
On May 16, 2024, at 4:00 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Al, I'm not sure if you mean you want to recolor the boxes on the sequence, or the corresponding parts of the 3D structure (if any) in the main graphics window.
(A) For the 3D structure: If you have a 3D structure associated with the sequence, then clicking the sequence region also automatically selects that part of the structure. The selected parts will be outlined with green in the main graphics window. If you don't know what I mean by "associated with" see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...>
You can use the Actions menu (e.g. Actions... Color... etc.) to act on your current selection in the 3D structure. Using the Actions menu generates the corresponding command and shows it in the Log, which is meant to help people learn the corresponding commands and also allow scripting these actions. Or, instead of using the menu, you could just enter the command directly. Generally to color the current selection regardless of how that selection was made, you would use the "color" command with "sel" to mean the current selection, e.g.
color sel hot pink target ar
"target ar" means color both the ribbons and atoms, "target r" would mean ribbons only, "target a" atoms only, etc. They may not be displayed at the time. To actually show the atoms you could again use the Actions menu (Actions... Atoms/Bonds... Show) or just use the corresponding command, e.g.
show sel
There is also undo/redo if you mess up and want to go back, via "undo" and "redo" commands or Edit menu.
There are help pages for all of these commands explaining their options. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>
(B) To recolor the boxes on the sequence, the GUI (rather than commands) is the way to go.
If you are using the UniProt sequence features dialog, click the color squares to open the system color editor and edit the color interactively. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot>
If you are not using the UniProt sequence features dialog, you can use the sequence window context menu Annotations... Regions... (show a context menu by right-click, or if Mac Ctrl-click on the tool, in this case the sequence window) to open the Region Browser, which also has color wells for changing the box interior and border colors. See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#regionbro...>
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
From: Allen Place <place@umces.edu> Date: May 16, 2024 at 5:11:31 AM PDT
Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. Al
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
_______________________________________________ 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/
Elaine, Do you know the criteria that AlphaFold3 uses for its 5 models that are reported? Model 0, etc. I can find what cutoffs are used. Also what is the color palette used my Chimerax? Al
On May 16, 2024, at 7:55 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Also it is not necessary to go through selection; if you're just going to use a command and you already know the structure residue number range(s) that you want, you can specify them directly in the command, for example:
color /A:48-66,125-138 orange
How to specify models, chains, residues, atoms in the command line:
<https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/comman...>
I hope this helps, Elaine
On May 16, 2024, at 4:00 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Al, I'm not sure if you mean you want to recolor the boxes on the sequence, or the corresponding parts of the 3D structure (if any) in the main graphics window.
(A) For the 3D structure: If you have a 3D structure associated with the sequence, then clicking the sequence region also automatically selects that part of the structure. The selected parts will be outlined with green in the main graphics window. If you don't know what I mean by "associated with" see: <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
You can use the Actions menu (e.g. Actions... Color... etc.) to act on your current selection in the 3D structure. Using the Actions menu generates the corresponding command and shows it in the Log, which is meant to help people learn the corresponding commands and also allow scripting these actions. Or, instead of using the menu, you could just enter the command directly. Generally to color the current selection regardless of how that selection was made, you would use the "color" command with "sel" to mean the current selection, e.g.
color sel hot pink target ar
"target ar" means color both the ribbons and atoms, "target r" would mean ribbons only, "target a" atoms only, etc. They may not be displayed at the time. To actually show the atoms you could again use the Actions menu (Actions... Atoms/Bonds... Show) or just use the corresponding command, e.g.
show sel
There is also undo/redo if you mess up and want to go back, via "undo" and "redo" commands or Edit menu.
There are help pages for all of these commands explaining their options. <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/index....>
(B) To recolor the boxes on the sequence, the GUI (rather than commands) is the way to go.
If you are using the UniProt sequence features dialog, click the color squares to open the system color editor and edit the color interactively. <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
If you are not using the UniProt sequence features dialog, you can use the sequence window context menu Annotations... Regions... (show a context menu by right-click, or if Mac Ctrl-click on the tool, in this case the sequence window) to open the Region Browser, which also has color wells for changing the box interior and border colors. See <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
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
From: Allen Place <place@umces.edu> Date: May 16, 2024 at 5:11:31 AM PDT
Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. Al
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://www.google.com/url?q=https://mail.cgl.ucsf.edu/mailman/archives/list...
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful” He is smart, makes friends easily, and never loses his sense of humour. He thrives on a challenge  Sign up to receive our quarterly newsletter, Inside IMET!
Hi Allen, The default coloring for showing alphafold models in ChimeraX is shown in the help here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring> See also discussion in recent posts -- this coloring is not the same as what may be shown in the AlphaFold database: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> The pLDDT confidence values are in the column of the PDB file that is normally used for b-factors, so you can recolor the model however you like with the "color bfactor" command and its "palette" options, as mentioned in the discussion above. For your other question, you may need to look at the information from the AlphaFold developers (their published papers and/or alphafold database website). I don't know the details of what score is used to figure out which of the five models is best. However, depending on how you are running the program, you may get all five and could look at the other ones. See for example this previous post <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 May 22, 2024, at 5:37 AM, Allen Place via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Elaine, Do you know the criteria that AlphaFold3 uses for its 5 models that are reported? Model 0, etc. I can find what cutoffs are used. Also what is the color palette used my Chimerax? Al
On May 16, 2024, at 7:55 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Also it is not necessary to go through selection; if you're just going to use a command and you already know the structure residue number range(s) that you want, you can specify them directly in the command, for example:
color /A:48-66,125-138 orange
How to specify models, chains, residues, atoms in the command line:
<https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/comman...>
I hope this helps, Elaine
On May 16, 2024, at 4:00 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Al, I'm not sure if you mean you want to recolor the boxes on the sequence, or the corresponding parts of the 3D structure (if any) in the main graphics window.
(A) For the 3D structure: If you have a 3D structure associated with the sequence, then clicking the sequence region also automatically selects that part of the structure. The selected parts will be outlined with green in the main graphics window. If you don't know what I mean by "associated with" see: <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
You can use the Actions menu (e.g. Actions... Color... etc.) to act on your current selection in the 3D structure. Using the Actions menu generates the corresponding command and shows it in the Log, which is meant to help people learn the corresponding commands and also allow scripting these actions. Or, instead of using the menu, you could just enter the command directly. Generally to color the current selection regardless of how that selection was made, you would use the "color" command with "sel" to mean the current selection, e.g.
color sel hot pink target ar
"target ar" means color both the ribbons and atoms, "target r" would mean ribbons only, "target a" atoms only, etc. They may not be displayed at the time. To actually show the atoms you could again use the Actions menu (Actions... Atoms/Bonds... Show) or just use the corresponding command, e.g.
show sel
There is also undo/redo if you mess up and want to go back, via "undo" and "redo" commands or Edit menu.
There are help pages for all of these commands explaining their options. <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/index....>
(B) To recolor the boxes on the sequence, the GUI (rather than commands) is the way to go.
If you are using the UniProt sequence features dialog, click the color squares to open the system color editor and edit the color interactively. <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
If you are not using the UniProt sequence features dialog, you can use the sequence window context menu Annotations... Regions... (show a context menu by right-click, or if Mac Ctrl-click on the tool, in this case the sequence window) to open the Region Browser, which also has color wells for changing the box interior and border colors. See <https://www.google.com/url?q=https://rbvi.ucsf.edu/chimerax/docs/user/tools/...>
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
From: Allen Place <place@umces.edu> Date: May 16, 2024 at 5:11:31 AM PDT
Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. Al
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://www.google.com/url?q=https://mail.cgl.ucsf.edu/mailman/archives/list...
Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu
ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful”
He is smart, makes friends easily, and never loses his sense of humour.
He thrives on a challenge
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participants (3)
-
Allen Place -
Elaine Meng -
Eric Pettersen