[chimerax-users] syntax on marker and marker link placement

[Tom Goddard]

Hi Joel,

  ChimeraX has trouble when a command has two model or atom specifiers next to each other in a command.  It considers them as a single argument, ignoring the space between them.  So we try to make our commands not take two adjacent specifier arguments.  So to fix this I just changed the marker command so you have to say "marker #2 position #1/A,B:10 at CA"  with the position keyword added.  This will be in tonight's builds.  The "marker segment" command also requires the "position" keyword now.

  You can circumvent the problem in your current ChimeraX using

	marker #2 /a,b:10 at CA color yellow radius 1

dropping the #1 from the atom specifier assuming you have no other structure with chains A,B open.  Surprisingly this works because the marker set specifier is only expecting a model so it doesn't merge the chain specifiers that follow.

	Tom


> On Apr 11, 2020, at 1:12 PM, Joel Meyerson wrote:
> 
> Hi,
> I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I get an error.
>  
> marker #2 #1/a,b:10 at CA color yellow radius 1
> marker #2 #1/a,b:20 at CA color yellow radius 1
> marker link #2:1,2 color yellow radius 0.5
>  
> Gives the error:
> Missing or invalid "position" argument: Expected 3 floats or object specifier
>  
> Any suggestions on how to fix the syntax, or is there an alternative approach?
>  
> Thanks,
> Joel
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