retrieving assigned color and ribbon thickness
Hi Elaine, I'm wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what's the RGB value I've assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
Hi Sumitro, You can use the Selection Inspector to get color RGB values. For example, you could Ctrl-click to select one residue's ribbon segment, then click the green magnifying glass on the lower right corner of the Chimera window to open the Selection Inspector, and then inspect "Residue" -- there will be a square color well with the ribbon color, and if you click that color well, the Color Editor will appear with that color in it, and sliders showing the RGB values. When you were originally setting the ribbon dimensions in the Ribbon Style Editor, if you saved the settings with a name, the name will be shown as the "ribbon scaling" in the Residue part of the Selection Inspector. You would have to reopen the Ribbon Style Editor and go to that name again to see what the corresponding dimensions were. If you didn't give the settings any name, however, I don't know of any easy way to figure out the exact dimensions. If you had a session file, it is embedded in there somewhere, but I don't know how to find it. Maybe someone else can advise on that point. However, clearly the better way if you are starting anew is to give the settings a name in the Ribbon Style Editor before applying them to the structure. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 3, 2011, at 9:40 PM, Sumitro Harjanto wrote:
Hi Elaine, I’m wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what’s the RGB value I’ve assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro
Hi Elaine, Actually, I use "render by attribute" tool to set (scale) the ribbons' ('Worms') thickness accordingly. So I din actually use the Ribbon style editor. I understand I should be able to find the absolute thickness of each residue in the session file (somewhere), but is there a relatively simple way to find out the scale I have used for the worms thickness..? It's not really a big problem, I can always estimate the scale again, so if it's complicated and having to dig deep into the session file then it's okay. =] thanks! Cheers, Sumitro -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, January 05, 2011 2:23 AM To: Sumitro Harjanto Cc: Chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] retrieving assigned color and ribbon thickness Hi Sumitro, You can use the Selection Inspector to get color RGB values. For example, you could Ctrl-click to select one residue's ribbon segment, then click the green magnifying glass on the lower right corner of the Chimera window to open the Selection Inspector, and then inspect "Residue" -- there will be a square color well with the ribbon color, and if you click that color well, the Color Editor will appear with that color in it, and sliders showing the RGB values. When you were originally setting the ribbon dimensions in the Ribbon Style Editor, if you saved the settings with a name, the name will be shown as the "ribbon scaling" in the Residue part of the Selection Inspector. You would have to reopen the Ribbon Style Editor and go to that name again to see what the corresponding dimensions were. If you didn't give the settings any name, however, I don't know of any easy way to figure out the exact dimensions. If you had a session file, it is embedded in there somewhere, but I don't know how to find it. Maybe someone else can advise on that point. However, clearly the better way if you are starting anew is to give the settings a name in the Ribbon Style Editor before applying them to the structure. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 3, 2011, at 9:40 PM, Sumitro Harjanto wrote:
Hi Elaine, I'm wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what's the RGB value I've assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro
Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
Hi Sumitro, It's doable, but requires some Python. Open IDLE (under General Controls) and type: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): vals = [r.ribbonStyle.size for r in m.residues] print m, min(vals), max(vals) The above will print the min/max scale used for each molecule model you have open. You could also put the above into a .py file (you would need to add "import chimera" as the first line though) and execute it using File->Open. The numbers would then be printed to the reply log. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 4, 2011, at 7:15 PM, Sumitro Harjanto wrote:
Hi Elaine,
Actually, I use "render by attribute" tool to set (scale) the ribbons' ('Worms') thickness accordingly. So I din actually use the Ribbon style editor. I understand I should be able to find the absolute thickness of each residue in the session file (somewhere), but is there a relatively simple way to find out the scale I have used for the worms thickness..?
It's not really a big problem, I can always estimate the scale again, so if it's complicated and having to dig deep into the session file then it's okay. =] thanks!
Cheers, Sumitro
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, January 05, 2011 2:23 AM To: Sumitro Harjanto Cc: Chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] retrieving assigned color and ribbon thickness
Hi Sumitro, You can use the Selection Inspector to get color RGB values. For example, you could Ctrl-click to select one residue's ribbon segment, then click the green magnifying glass on the lower right corner of the Chimera window to open the Selection Inspector, and then inspect "Residue" -- there will be a square color well with the ribbon color, and if you click that color well, the Color Editor will appear with that color in it, and sliders showing the RGB values.
When you were originally setting the ribbon dimensions in the Ribbon Style Editor, if you saved the settings with a name, the name will be shown as the "ribbon scaling" in the Residue part of the Selection Inspector. You would have to reopen the Ribbon Style Editor and go to that name again to see what the corresponding dimensions were. If you didn't give the settings any name, however, I don't know of any easy way to figure out the exact dimensions. If you had a session file, it is embedded in there somewhere, but I don't know how to find it. Maybe someone else can advise on that point. However, clearly the better way if you are starting anew is to give the settings a name in the Ribbon Style Editor before applying them to the structure.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 3, 2011, at 9:40 PM, Sumitro Harjanto wrote:
Hi Elaine, I'm wondering if it is possible to retrieve the numerical (RGB) values of the color & ribbon width that I have previously assigned to certain residue(s). I often try out a certain color and save it in a session, but when I come back to the session and try to apply the color to the other residues I realized I forgot what's the RGB value I've assigned and have to resort to visual inspection (which is not very accurate). The same problem I have experienced with the ribbon thickness. Is there a way for me to keep a record of / retrieve these values? Thanks! Cheers, Sumitro
Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Sumitro Harjanto