[chimerax-users] Render psuedobonds for RMF models?

[Tom Goddard]

Hi Matthew,

  Yes.  The coarse grain models made from reading RMF files create spheres that are actually atoms, and any atoms can be connected by pseudobonds.  I don't know much about RMF in Chimera and ChimeraX. Ben Webb and Conrad Huang worked on that and Conrad retired 2 years ago.  It may be that reading RMF creates pseudobonds that are specified in the RMF file.  Another way to create pseudobonds is to open a pseudobond file

	https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>

For that you need to figure out the names of the "atoms" (which may represent coarse grain beads) you want to connect.  You can open the RMF and hover the mouse over a sphere and a popup will show its name.  Also the ChimeraX distance command can create pseudobonds

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html

  Tom


> On Apr 19, 2022, at 8:41 AM, Hancock, Matthew  wrote:
> 
> This Message Is From an External Sender
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> Hi Tom, 
> 
> I am a UCSF graduate student in Andrej Sali's group and have a question about Chimera/ChimeraX functionality. I am curious if it is possible to render psuedobonds for multi-scale structures that are read from RMF files. Similar to how it can be done for pdb structures.
> 
> Best
> Matthew 

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