[chimerax-users] Assessment of labeling data using ChimeraX

[Elaine Meng]

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