Assessment of labeling data using ChimeraX
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
Hi Alessio, I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific. However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms. distance command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> pseudobond input file <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
Dear Elaine Meng, thanks for the quick answer. This program allows you to analyze different kind of structural MS data and gives you a txt file in which are reported in my case labeling yield for each residue both in absolute way or as protection factor when comparing two different Protein states (e.g. with and without a Ligand for example). They say this file can be easily used by ChimeraX using the define by Attribute command since These are numerical values for a given residue in your Protein of interest. But I am not able to make it readable by the software. Hope you can help me out with this Best wishes Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224 From: Elaine Meng Sent: 14 January 2022 18:19 To: Alessio Di Ianni Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX Hi Alessio, I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific. However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms. distance command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> pseudobond input file <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
Hi Alessio, Then they are "attribute assignment files" as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> Those can be read by both Chimera and ChimeraX. Since you're using ChimeraX, the rest of this message refers to ChimeraX. As mentioned in the link above, you just use the "open" command to open such a file (with the corresponding 3D structure(s) already open) and that will automatically assign the attribute. You can either name those files something.defattr so that the format will be known automatically, or if you keep the .txt at the end of the name, use the "format defattr" option in the "open" command. Then after the attribute is assigned, you can refer to it by name in the command line, e.g. command "color byattribute" or "select" using an attribute value range, see these links: <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> ...specifying attribute value ranges in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> For example, to select atoms with bfactor attribute values over 40: select @@bfactor>40 The attribute name in the files is really long (look at the file contents with a text editor to see) and you may want to text-edit the file to change it to something more convenient before you assign the attribute. Again, the format of the file is described in the first link in this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2022, at 12:30 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine Meng, thanks for the quick answer. This program allows you to analyze different kind of structural MS data and gives you a txt file in which are reported in my case labeling yield for each residue both in absolute way or as protection factor when comparing two different Protein states (e.g. with and without a Ligand for example). They say this file can be easily used by ChimeraX using the define by Attribute command since These are numerical values for a given residue in your Protein of interest. But I am not able to make it readable by the software. Hope you can help me out with this Best wishes
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
From: Elaine Meng Sent: 14 January 2022 18:19 To: Alessio Di Ianni Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX
Hi Alessio, I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific.
However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms.
distance command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
pseudobond input file <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
<p53_labeling_absolute.txt><p53_labeling_p_factor.txt>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, thanks a lot for the help, I was able to visualize the labeling Information in the pdb. If I have a homooligomer, how should I do it If I have always the same residues? Should I introduce a chain specifier in my .defattr file? Thanks a lot for the help Best wishes Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224 From: Elaine Meng Sent: 17 January 2022 20:32 To: Alessio Di Ianni Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX Hi Alessio, Then they are "attribute assignment files" as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> Those can be read by both Chimera and ChimeraX. Since you're using ChimeraX, the rest of this message refers to ChimeraX. As mentioned in the link above, you just use the "open" command to open such a file (with the corresponding 3D structure(s) already open) and that will automatically assign the attribute. You can either name those files something.defattr so that the format will be known automatically, or if you keep the .txt at the end of the name, use the "format defattr" option in the "open" command. Then after the attribute is assigned, you can refer to it by name in the command line, e.g. command "color byattribute" or "select" using an attribute value range, see these links: <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> ...specifying attribute value ranges in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes> For example, to select atoms with bfactor attribute values over 40: select @@bfactor>40 The attribute name in the files is really long (look at the file contents with a text editor to see) and you may want to text-edit the file to change it to something more convenient before you assign the attribute. Again, the format of the file is described in the first link in this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2022, at 12:30 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine Meng, thanks for the quick answer. This program allows you to analyze different kind of structural MS data and gives you a txt file in which are reported in my case labeling yield for each residue both in absolute way or as protection factor when comparing two different Protein states (e.g. with and without a Ligand for example). They say this file can be easily used by ChimeraX using the define by Attribute command since These are numerical values for a given residue in your Protein of interest. But I am not able to make it readable by the software. Hope you can help me out with this Best wishes
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
From: Elaine Meng Sent: 14 January 2022 18:19 To: Alessio Di Ianni Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX
Hi Alessio, I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific.
However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms.
distance command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
pseudobond input file <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
<p53_labeling_absolute.txt><p53_labeling_p_factor.txt>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Alessio, Yes, the specifier in the attribute file is the same as what could be used in the command line, so it can contain model number, chain ID, residue number, atom name, etc. You can test that the specifier gets what you want by putting it in a command, e.g. select /A:10 ...if that selects the atoms or residue that you want, then "/A:10" would work inside your attribute file too. Command-line atom specification: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Best, Elaine
On Jan 20, 2022, at 3:47 AM, Alessio Di Ianni <alessio.di-ianni@pharmazie.uni-halle.de> wrote:
Hi Elaine, thanks a lot for the help, I was able to visualize the labeling Information in the pdb. If I have a homooligomer, how should I do it If I have always the same residues? Should I introduce a chain specifier in my .defattr file? Thanks a lot for the help
Best wishes
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
From: Elaine Meng Sent: 17 January 2022 20:32 To: Alessio Di Ianni Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX
Hi Alessio, Then they are "attribute assignment files" as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
Those can be read by both Chimera and ChimeraX. Since you're using ChimeraX, the rest of this message refers to ChimeraX.
As mentioned in the link above, you just use the "open" command to open such a file (with the corresponding 3D structure(s) already open) and that will automatically assign the attribute. You can either name those files something.defattr so that the format will be known automatically, or if you keep the .txt at the end of the name, use the "format defattr" option in the "open" command.
Then after the attribute is assigned, you can refer to it by name in the command line, e.g. command "color byattribute" or "select" using an attribute value range, see these links: <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> ...specifying attribute value ranges in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>
For example, to select atoms with bfactor attribute values over 40: select @@bfactor>40
The attribute name in the files is really long (look at the file contents with a text editor to see) and you may want to text-edit the file to change it to something more convenient before you assign the attribute. Again, the format of the file is described in the first link in this message.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 17, 2022, at 12:30 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine Meng, thanks for the quick answer. This program allows you to analyze different kind of structural MS data and gives you a txt file in which are reported in my case labeling yield for each residue both in absolute way or as protection factor when comparing two different Protein states (e.g. with and without a Ligand for example). They say this file can be easily used by ChimeraX using the define by Attribute command since These are numerical values for a given residue in your Protein of interest. But I am not able to make it readable by the software. Hope you can help me out with this Best wishes
Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224
From: Elaine Meng Sent: 14 January 2022 18:19 To: Alessio Di Ianni Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX
Hi Alessio, I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific.
However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms.
distance command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
pseudobond input file <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards
participants (2)
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Alessio Di Ianni -
Elaine Meng