[chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization

[Elaine Meng]

Hi Pascal,
Many features are are still in development, so although we can easily imagine useful features (and we welcome your suggestions), many are not yet implemented.

Yes, you can load different sets of crosslinks.  The “pseudobond” input format is just plain text specifiying pairs of atoms.  
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>

Then you can specify the different models (input file -> model) in the “crosslinks histogram” command by their numbers as shown in the Models panel, e.g.

crosslinks hist #1.3
crosslinks hist #3

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>

Currently there isn’t color-by-length or selection-by-length, sorry.  The interaction with the histogram that you may already have seen is that passing the cursor over the columns of the histogram temporarily enlarges the corresponding-length pseudobonds and hides the others.  There isn’t control over how wide the histogram bars are.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Sep 1, 2018, at 2:57 AM, Pascal Albanese <pascal.albanese at polito.it> wrote:
> 
> Dear Support Staff, 
> 
> first of all many thanks for developing Chimera!
> 
> I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them):
> 
> - Is it possible to load different sets of distances/crosslinks (like with different IDs)?
> - is it possible to color code the distances with a cutoff (like red if >30 for instance)?
> - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...)
> 
> that's it, maybe something can be done writing the code but unfortunately it's not my job. 
> 
> Thanks a lot and looking forward to hear from you, 
> 
> Cheers, 
> Pascal