Color a surface by seq_conservation of neighboring residues
Hi,
my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor.
Thanks for any advice.
Lothar
NIH
Hi Lothar, If it is a molecular surface, it would be done in just the same way as coloring the atoms or cartoons by attribute. After ascertaining the presence of a seq_conservation attribute (e.g. by opening a sequence alignment, showing a conservation header calculated using the method of your choice, and making sure your structure is associated, you would just show the molecular surface and then use "color byattribute" or the "Render by Attribute" dialog to do coloring by conservation.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html
Our coloring by conservation tutorial was written before we had the Render by Attribute tool, but it shows the commands. The first example is coloring the molecular surface by residue conservation: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html
If it's not a molecular surface, but EM map isosurface or something like that, you could color the atoms by conservation and then use "color zone" to make the map surface match the nearby atoms. https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Also Chimera/ChimeraX avoid the annoyance of having to create a bunch of PDB files with the value of interest in the b-factor column. You can just assign multiple attributes either by using tools in the program (like the sequence alignment viewer) or reading them in via a separate "attribute assignment file," in the case of arbitrary values calculated with some outside mechanism. Or, you can assign one value at a time with "setattr" which would typically be done in a script file (.cxc file).
https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html
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 22, 2024, at 6:51 AM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor.
Thanks for any advice.
Lothar
Hi,
I guess I wasn't clear. Maybe I asked too much in one e-mail. Let me ask this, ChimeraX calculates sequence conservation from an aln file and assigns the values to atom attributes. Can I write out the numerical values of what ChimeraX had calculated for, say verification ? Thanks, Lothar
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, March 22, 2024 11:26 AM To: Esser, Lothar (NIH/NCI) [E] esserlo@mail.nih.gov Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Color a surface by seq_conservation of neighboring residues
Hi Lothar, If it is a molecular surface, it would be done in just the same way as coloring the atoms or cartoons by attribute. After ascertaining the presence of a seq_conservation attribute (e.g. by opening a sequence alignment, showing a conservation header calculated using the method of your choice, and making sure your structure is associated, you would just show the molecular surface and then use "color byattribute" or the "Render by Attribute" dialog to do coloring by conservation.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html
Our coloring by conservation tutorial was written before we had the Render by Attribute tool, but it shows the commands. The first example is coloring the molecular surface by residue conservation: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html
If it's not a molecular surface, but EM map isosurface or something like that, you could color the atoms by conservation and then use "color zone" to make the map surface match the nearby atoms. https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Also Chimera/ChimeraX avoid the annoyance of having to create a bunch of PDB files with the value of interest in the b-factor column. You can just assign multiple attributes either by using tools in the program (like the sequence alignment viewer) or reading them in via a separate "attribute assignment file," in the case of arbitrary values calculated with some outside mechanism. Or, you can assign one value at a time with "setattr" which would typically be done in a script file (.cxc file).
https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html
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 22, 2024, at 6:51 AM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor.
Thanks for any advice.
Lothar
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Hi Lothar, Sure, you can save the values of an attribute, in this case the residue attribute named "seq_conservation", to a text file. See "save" command and its options for saving an attribute file:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html
This is the same format in which you could read/assign in your own values calculated in some external program.
Or if you don't want to bother writing a file, you could write the values to the Log with command:
info residues attribute seq_conservation
https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html
By the way, you can change the sequence conservation calculation method and parameters in the Settings of the Sequence Viewer, see:
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 Mar 22, 2024, at 3:28 PM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I guess I wasn't clear. Maybe I asked too much in one e-mail. Let me ask this, ChimeraX calculates sequence conservation from an aln file and assigns the values to atom attributes. Can I write out the numerical values of what ChimeraX had calculated for, say verification ? Thanks, Lothar
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, March 22, 2024 11:26 AM To: Esser, Lothar (NIH/NCI) [E] esserlo@mail.nih.gov Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Color a surface by seq_conservation of neighboring residues
Hi Lothar, If it is a molecular surface, it would be done in just the same way as coloring the atoms or cartoons by attribute. After ascertaining the presence of a seq_conservation attribute (e.g. by opening a sequence alignment, showing a conservation header calculated using the method of your choice, and making sure your structure is associated, you would just show the molecular surface and then use "color byattribute" or the "Render by Attribute" dialog to do coloring by conservation.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html
Our coloring by conservation tutorial was written before we had the Render by Attribute tool, but it shows the commands. The first example is coloring the molecular surface by residue conservation: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html
If it's not a molecular surface, but EM map isosurface or something like that, you could color the atoms by conservation and then use "color zone" to make the map surface match the nearby atoms. https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Also Chimera/ChimeraX avoid the annoyance of having to create a bunch of PDB files with the value of interest in the b-factor column. You can just assign multiple attributes either by using tools in the program (like the sequence alignment viewer) or reading them in via a separate "attribute assignment file," in the case of arbitrary values calculated with some outside mechanism. Or, you can assign one value at a time with "setattr" which would typically be done in a script file (.cxc file).
https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html
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 22, 2024, at 6:51 AM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor.
Thanks for any advice.
Lothar
Hi, thanks. I missed that.
Lothar ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, March 22, 2024 6:44 PM To: Esser, Lothar (NIH/NCI) [E] esserlo@mail.nih.gov Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Color a surface by seq_conservation of neighboring residues
Hi Lothar, Sure, you can save the values of an attribute, in this case the residue attribute named "seq_conservation", to a text file. See "save" command and its options for saving an attribute file:
<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
This is the same format in which you could read/assign in your own values calculated in some external program.
Or if you don't want to bother writing a file, you could write the values to the Log with command:
info residues attribute seq_conservation
<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html>
By the way, you can change the sequence conservation calculation method and parameters in the Settings of the Sequence Viewer, see:
<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....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 Mar 22, 2024, at 3:28 PM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I guess I wasn't clear. Maybe I asked too much in one e-mail. Let me ask this, ChimeraX calculates sequence conservation from an aln file and assigns the values to atom attributes. Can I write out the numerical values of what ChimeraX had calculated for, say verification ? Thanks, Lothar
-----Original Message----- From: Elaine Meng meng@cgl.ucsf.edu Sent: Friday, March 22, 2024 11:26 AM To: Esser, Lothar (NIH/NCI) [E] esserlo@mail.nih.gov Cc: chimerax-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [chimerax-users] Color a surface by seq_conservation of neighboring residues
Hi Lothar, If it is a molecular surface, it would be done in just the same way as coloring the atoms or cartoons by attribute. After ascertaining the presence of a seq_conservation attribute (e.g. by opening a sequence alignment, showing a conservation header calculated using the method of your choice, and making sure your structure is associated, you would just show the molecular surface and then use "color byattribute" or the "Render by Attribute" dialog to do coloring by conservation.
<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>
Our coloring by conservation tutorial was written before we had the Render by Attribute tool, but it shows the commands. The first example is coloring the molecular surface by residue conservation: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.u...https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html>
If it's not a molecular surface, but EM map isosurface or something like that, you could color the atoms by conservation and then use "color zone" to make the map surface match the nearby atoms. <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
Also Chimera/ChimeraX avoid the annoyance of having to create a bunch of PDB files with the value of interest in the b-factor column. You can just assign multiple attributes either by using tools in the program (like the sequence alignment viewer) or reading them in via a separate "attribute assignment file," in the case of arbitrary values calculated with some outside mechanism. Or, you can assign one value at a time with "setattr" which would typically be done in a script file (.cxc file).
<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
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 22, 2024, at 6:51 AM, Esser, Lothar (NIH/NCI) [E] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor.
Thanks for any advice.
Lothar
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
participants (2)
-
Elaine Meng -
Esser, Lothar (NIH/NCI) [E]