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#8434 closed enhancement (not a bug)
Rainbow and color sequential
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Hello, The rainbow and color sequential command do not work on atom and bond targets, only cartoon and surface. Can this be fixed? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Change History (8)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Type: | defect → enhancement |
comment:3 by , 3 years ago
I'm not sure what you are asking for. If you want to rainbow color only atoms and not ribbon you can use command "rainbow target a", I tested it works. If you mean you want to type "rainbow atoms", that doesn't really make sense given the current syntax of the command because the first argument is specifying what parameter the color is varying over, residue number, chain id, structure id. If you mean you want to color only bonds and not atoms with "rainbow target b". That is not working currently. No one has ever requested that. Normally bonds are colored according to their atoms. So you would also have to change the bond coloring mode using "color halfbond false".
follow-up: 4 comment:4 by , 3 years ago
Sorry for not clarifying. I'd like to color sequentially at the level of chain, but I want the color to register on all targets abcs. When I execute this: color sequential chain targ abcs palette 1473 The open pdb does not register the color on the atom and bonds. Does this make sense? Thank you, Matt On 2/3/23, 5:11 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote: EXTERNAL EMAIL– Use caution with any links or file attachments. #8434: Rainbow and color sequential -------------------------------------+------------------------- Reporter: matt.jaremko@… | Owner: Tom Goddard Type: enhancement | Status: assigned Priority: normal | Milestone: Component: Depiction | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | -------------------------------------+------------------------- Comment (by Tom Goddard): I'm not sure what you are asking for. If you want to rainbow color only atoms and not ribbon you can use command "rainbow target a", I tested it works. If you mean you want to type "rainbow atoms", that doesn't really make sense given the current syntax of the command because the first argument is specifying what parameter the color is varying over, residue number, chain id, structure id. If you mean you want to color only bonds and not atoms with "rainbow target b". That is not working currently. No one has ever requested that. Normally bonds are colored according to their atoms. So you would also have to change the bond coloring mode using "color halfbond false". -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:3> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:3>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/>> ChimeraX Issue Tracker This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
comment:5 by , 3 years ago
Thanks for the clarification. That makes sense. But it works fine for me.
open 2qke
color sequential chain targ abcs palette 1473
This colors the atoms and bonds in ChimeraX 1.5. In fact the "targ abcs" is not necessary since all objects are colored if target is not specified.
follow-up: 6 comment:6 by , 3 years ago
Hi Tom, Atoms and bonds are colored for the sidechains, but not for ligands. At least for me on ChimeraX 1.5. Have you attempted this with ligands? Thank you, Matt On 2/3/23, 5:34 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote: EXTERNAL EMAIL– Use caution with any links or file attachments. #8434: Rainbow and color sequential -------------------------------------+------------------------- Reporter: matt.jaremko@… | Owner: Tom Goddard Type: enhancement | Status: assigned Priority: normal | Milestone: Component: Depiction | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | -------------------------------------+------------------------- Comment (by Tom Goddard): Thanks for the clarification. That makes sense. But it works fine for me. open 2qke color sequential chain targ abcs palette 1473 This colors the atoms and bonds in ChimeraX 1.5. In fact the "targ abcs" is not necessary since all objects are colored if target is not specified. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:5> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:5>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/>> ChimeraX Issue Tracker This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
comment:7 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
The rainbow chain or color sequential chain command colors only the atoms of polymer chains. It is a bit confusing that sometimes "chain" in ChimeraX means polymer (ie poly-peptide or poly-nucleotide) as in this case, and sometimes it means "chain identifier" from the PDB file which can of course non-polymer ligands.
The command seems to be behaving as intended. The documentation for color sequential says
"chains – a different color for each biopolymer chain in an atomic model; non-biopolymer residues are not affected"
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential
You can use "color bychain" to color all atoms for each chain identifier differently, although it uses a fixed set of colors and does not let you choose a palette.
follow-up: 8 comment:8 by , 3 years ago
Thanks for the clarification Tom. Matt On 2/6/23, 2:12 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote: EXTERNAL EMAIL– Use caution with any links or file attachments. #8434: Rainbow and color sequential -------------------------------------+------------------------- Reporter: matt.jaremko@… | Owner: Tom Goddard Type: enhancement | Status: closed Priority: normal | Milestone: Component: Depiction | Version: Resolution: not a bug | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | -------------------------------------+------------------------- Changes (by Tom Goddard): * status: assigned => closed * resolution: => not a bug Comment: The rainbow chain or color sequential chain command colors only the atoms of polymer chains. It is a bit confusing that sometimes "chain" in ChimeraX means polymer (ie poly-peptide or poly-nucleotide) as in this case, and sometimes it means "chain identifier" from the PDB file which can of course non-polymer ligands. The command seems to be behaving as intended. The documentation for color sequential says "chains – a different color for each biopolymer chain in an atomic model; non-biopolymer residues are not affected" https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential> You can use "color bychain" to color all atoms for each chain identifier differently, although it uses a fixed set of colors and does not let you choose a palette. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:7> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8434#comment:7>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/>> ChimeraX Issue Tracker This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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