Hi there!
I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades.
Thanks,
Renee
Hi Renee, I don't think I understand your question. Pseudobond files (pb files) and color keys can both have any colors, including defined with hex codes, etc., and those two things (pseudobonds and color keys) are not tied together in any way.
Also you mention "confidence" which makes me think maybe you are talking about AlphaFold-predicted structures and maybe PDB files instead of "pb" files. PDB files just contain the structures (3D atomic coordinates) and don't have colors in them, although of course you can display them in ChimeraX with whatever colors you like. If you are displaying AlphaFold-predicted structures, there is a default ribbon coloring which maps to pLDDT confidence values, and the color key can show that default coloring:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring
But again, you can color them any way you want, and you can also make a color key that shows any colors that you want.
The pLDDT values are put into the B-factor column of a PDB file, so if you open an alphafold-predicted PDB file you can use the ChimeraX "color bfactor" command and with the "palette" option of that command, specify whatever colors and color->bfactor value mapping that you like, and with the "key" option of that command, automatically create a color key that matches whatever palette coloring that you specified. The command and its options are explained in the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
The coloring by attribute such as bfactor value in ChimeraX is gradual, i.e. in the default pLDDT confidence coloring, pLDDT 100 = blue and 90 = cornflower blue, and values in between 100 and 90 are between blue and cornflower blue, and that is shown by the color key.
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 Mar 13, 2024, at 5:35 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi there!
I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades.
Thanks, Renee
Hi Elaine,
thank you so much for getting back to me - sorry I wasn't very clear. You are correct about it being an alphafold prediction.
after using the command alphafold contacts /A to /B, I save the pb file (Interatomic pseudobonds(*.pb)) and get something like this:
; radius = 0.2 /A:61@CA /B:60@CA #141dfbff /A:40@CA /B:88@CA #2132f8ff /A:117@CA /B:1@CA #4b70f1ff /A:48@CA /B:36@CA #141efbff /A:51@CA /B:33@CA #1a27faff /
The last column are the colors and I believe most of these are different shades of blue. With what you explained to me and me re-reading the page on Pseudobonds Colored by PAE, this is making a lot more sense, and I think I will play with the commands.
Thank you! -Renee
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, March 13, 2024 6:54 PM To: Renee Garza Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about pb file
Hi Renee, I don't think I understand your question. Pseudobond files (pb files) and color keys can both have any colors, including defined with hex codes, etc., and those two things (pseudobonds and color keys) are not tied together in any way.
Also you mention "confidence" which makes me think maybe you are talking about AlphaFold-predicted structures and maybe PDB files instead of "pb" files. PDB files just contain the structures (3D atomic coordinates) and don't have colors in them, although of course you can display them in ChimeraX with whatever colors you like. If you are displaying AlphaFold-predicted structures, there is a default ribbon coloring which maps to pLDDT confidence values, and the color key can show that default coloring:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring
But again, you can color them any way you want, and you can also make a color key that shows any colors that you want.
The pLDDT values are put into the B-factor column of a PDB file, so if you open an alphafold-predicted PDB file you can use the ChimeraX "color bfactor" command and with the "palette" option of that command, specify whatever colors and color->bfactor value mapping that you like, and with the "key" option of that command, automatically create a color key that matches whatever palette coloring that you specified. The command and its options are explained in the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
The coloring by attribute such as bfactor value in ChimeraX is gradual, i.e. in the default pLDDT confidence coloring, pLDDT 100 = blue and 90 = cornflower blue, and values in between 100 and 90 are between blue and cornflower blue, and that is shown by the color key.
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 Mar 13, 2024, at 5:35 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi there!
I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades.
Thanks, Renee
Hi Renee,
If you are interested in seeing the Alphafold predicted aligned error (PAE) values between the residues at a protein-protein interface the "alphafold contacts" command can output a text file listing the pairs of residues with the exact values
alphafold contacts /A to /B output paevalues.txt
and the text file lines look like
/A:1 /B:478 13.74 /A:1 /B:480 9.30 /A:2 /B:480 7.65 /A:3 /B:481 8.39 ...
Here is the alphafold contacts documentation
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contact...
Tom
On Mar 13, 2024, at 7:31 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, thank you so much for getting back to me - sorry I wasn't very clear. You are correct about it being an alphafold prediction.
after using the command alphafold contacts /A to /B, I save the pb file (Interatomic pseudobonds(*.pb)) and get something like this: ; radius = 0.2 /A:61@CA /B:60@CA #141dfbff /A:40@CA /B:88@CA #2132f8ff /A:117@CA /B:1@CA #4b70f1ff /A:48@CA /B:36@CA #141efbff /A:51@CA /B:33@CA #1a27faff /
The last column are the colors and I believe most of these are different shades of blue. With what you explained to me and me re-reading the page on Pseudobonds Colored by PAE, this is making a lot more sense, and I think I will play with the commands.
Thank you! -Renee
From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, March 13, 2024 6:54 PM To: Renee Garza Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about pb file
Hi Renee, I don't think I understand your question. Pseudobond files (pb files) and color keys can both have any colors, including defined with hex codes, etc., and those two things (pseudobonds and color keys) are not tied together in any way.
Also you mention "confidence" which makes me think maybe you are talking about AlphaFold-predicted structures and maybe PDB files instead of "pb" files. PDB files just contain the structures (3D atomic coordinates) and don't have colors in them, although of course you can display them in ChimeraX with whatever colors you like. If you are displaying AlphaFold-predicted structures, there is a default ribbon coloring which maps to pLDDT confidence values, and the color key can show that default coloring:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring >
But again, you can color them any way you want, and you can also make a color key that shows any colors that you want.
The pLDDT values are put into the B-factor column of a PDB file, so if you open an alphafold-predicted PDB file you can use the ChimeraX "color bfactor" command and with the "palette" option of that command, specify whatever colors and color->bfactor value mapping that you like, and with the "key" option of that command, automatically create a color key that matches whatever palette coloring that you specified. The command and its options are explained in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute >
The coloring by attribute such as bfactor value in ChimeraX is gradual, i.e. in the default pLDDT confidence coloring, pLDDT 100 = blue and 90 = cornflower blue, and values in between 100 and 90 are between blue and cornflower blue, and that is shown by the color key.
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 Mar 13, 2024, at 5:35 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi there!
I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades.
Thanks, Renee
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/
Hi Tom,
Thank you so much - this is perfect!
-Renee
________________________________ From: Tom Goddard goddard@sonic.net Sent: Monday, April 1, 2024 1:21 PM To: Renee Garza Cc: ChimeraX Users Help Subject: Re: [chimerax-users] question about pb file
Hi Renee,
If you are interested in seeing the Alphafold predicted aligned error (PAE) values between the residues at a protein-protein interface the "alphafold contacts" command can output a text file listing the pairs of residues with the exact values
alphafold contacts /A to /B output paevalues.txt
and the text file lines look like
/A:1 /B:478 13.74 /A:1 /B:480 9.30 /A:2 /B:480 7.65 /A:3 /B:481 8.39 ...
Here is the alphafold contacts documentation
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contact...https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html*contacts__;Iw!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!03Wn0BjE-m9N2F314Tdxiptnk1OczYKi3oibMYvi7Ka-2yBqDjxomiIE5bEcJ8Ig0YZqpxcqJWYFebU$
Tom
On Mar 13, 2024, at 7:31 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, thank you so much for getting back to me - sorry I wasn't very clear. You are correct about it being an alphafold prediction.
after using the command alphafold contacts /A to /B, I save the pb file (Interatomic pseudobonds(*.pb)) and get something like this:
; radius = 0.2 /A:61@CA /B:60@CA #141dfbff /A:40@CA /B:88@CA #2132f8ff /A:117@CA /B:1@CA #4b70f1ff /A:48@CA /B:36@CA #141efbff /A:51@CA /B:33@CA #1a27faff /
The last column are the colors and I believe most of these are different shades of blue. With what you explained to me and me re-reading the page on Pseudobonds Colored by PAE, this is making a lot more sense, and I think I will play with the commands.
Thank you! -Renee
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, March 13, 2024 6:54 PM To: Renee Garza Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about pb file
Hi Renee, I don't think I understand your question. Pseudobond files (pb files) and color keys can both have any colors, including defined with hex codes, etc., and those two things (pseudobonds and color keys) are not tied together in any way.
Also you mention "confidence" which makes me think maybe you are talking about AlphaFold-predicted structures and maybe PDB files instead of "pb" files. PDB files just contain the structures (3D atomic coordinates) and don't have colors in them, although of course you can display them in ChimeraX with whatever colors you like. If you are displaying AlphaFold-predicted structures, there is a default ribbon coloring which maps to pLDDT confidence values, and the color key can show that default coloring:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloringhttps://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*coloring__;Iw!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!03Wn0BjE-m9N2F314Tdxiptnk1OczYKi3oibMYvi7Ka-2yBqDjxomiIE5bEcJ8Ig0YZqpxcqbytLAsI$ >
But again, you can color them any way you want, and you can also make a color key that shows any colors that you want.
The pLDDT values are put into the B-factor column of a PDB file, so if you open an alphafold-predicted PDB file you can use the ChimeraX "color bfactor" command and with the "palette" option of that command, specify whatever colors and color->bfactor value mapping that you like, and with the "key" option of that command, automatically create a color key that matches whatever palette coloring that you specified. The command and its options are explained in the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattributehttps://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html*byattribute__;Iw!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!03Wn0BjE-m9N2F314Tdxiptnk1OczYKi3oibMYvi7Ka-2yBqDjxomiIE5bEcJ8Ig0YZqpxcqTtGz_EI$ >
The coloring by attribute such as bfactor value in ChimeraX is gradual, i.e. in the default pLDDT confidence coloring, pLDDT 100 = blue and 90 = cornflower blue, and values in between 100 and 90 are between blue and cornflower blue, and that is shown by the color key.
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 Mar 13, 2024, at 5:35 PM, Renee Garza via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi there!
I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades.
Thanks, Renee
_______________________________________________ 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/https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!GX6Nv3_Pjr8b-17qtCok029Ok438DqXQ!03Wn0BjE-m9N2F314Tdxiptnk1OczYKi3oibMYvi7Ka-2yBqDjxomiIE5bEcJ8Ig0YZqpxcqmW8-PCM$
participants (3)
-
Elaine Meng -
Renee Garza -
Tom Goddard