[Chimera-users] rmf3 control in Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 15 15:20:45 PST 2019

Hi Daniel,
The "filename/nodename1/nodename2/nodename3” string is not an example of “rmfalias" command you would give, but the aliases that would be created as a result of your using that command.

rmfalias command:

RMF Viewer GUI:

The idea is that after creating those aliases with the “rmfalias” command, you could use them in other commands like “color,” etc.

All the square brackets in the usage mean optional things.  It looks like the thing you have highlighted is level 6 and maybe you want to omit some higher levels from the resulting aliases, so maybe something like 

rmfalias depth 7 skip_prefix 3

and then the aliases to use in other commands would be something like


for example, command:

color red EED/Frag_3-78/Frag_3-78/3-22_bead

I may be off by one in the numbers for the command options, but you can experiment and see what aliases you get (they are listed in the Reply Log) and adjust as needed.

Once you have the aliases, another issue might be which commands will work on them.  Several commands were implemented for atomic structures, and may only work at node levels implemented as atoms.  For example, the “distance” command adds a distance measurement between two atoms, and attribute assignment is to atoms, residues, or models. 

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 14, 2019, at 4:00 PM, Daniel Ziemianowicz <dziemian at ucalgary.ca> wrote:
> Hello, 
> I can’t find anything about this online, but I was told that there should be some control on the components of rmf3 files. Specifically, I would like to map my data onto an rmf structure from IMP. Normally I would use render/define attribute for some types of data and xlinkanalyzer plugin for crosslink data. 
> However, I can’t quite figure out how to control rmf structures in this same manner. I am hoping I could do something like this: given a bead with residue x and another bead containing residue y, I can map a crosslink to those beads. Likewise, with render by attribute, I can color the beads containing the relevant residues.
> The farthest I was able to get was reading the rmfalias documentation but that is also a bit confusing and I was not able to perform the aliasing – specifically it says
> rmfalias [ depth N ] [ skip_prefix M ] [ rmf filename ]
> as the command but then it gives an example
> filename/nodename1/nodename2/nodename3
> which seems to contradict the “usage” format. Either way I was not able to select or alias-name the beads I would like. Below I attached an example of the hierarchy in my file, how can I select e.g. “13-22_bead” of “EED”?
> I hope this was not a confusing question, let me know if I need to clarify. I can also email Ben Webb from the Sali lab if this is more relevant for them.
> Thank you, 
> Dan 
> <image001.png>
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