[chimerax-users] Assessment of labeling data using ChimeraX

[Alessio Di Ianni]

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 at 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 at 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


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