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

[Tom Goddard]

Ok.  The hack I suggested of "marker #2 /a,b:10 at CA" in fact does not work and confuses the marker command into making a new model #2 each time you run it even though model #2 already exists, because no markerset #2/A exists.  It should have given an error about this.  You'll need to get get tomorrow's fixed marker command and use the "position" keyword.

	Tom

> On Apr 11, 2020, at 1:56 PM, Joel Meyerson <jrm2008 at med.cornell.edu> wrote:
> 
> Hi Tom,
> Thanks for the info and the hack. I just tested it out I can display both markers. However, strangely enough the second marker seems not to appear as an entry in the model panel and when I try to create the marker link using the command in my previous email I get this error:
>  
> marker link command requires exactly 2 markers, got 1
>  
> Thanks also for introducing a change in the dailyo  release. I’ll be sure to test it.
>  
> Best,
> Joel
>  
> From: Tom Goddard <goddard at sonic.net>
> Date: Saturday, April 11, 2020 at 4:41 PM
> To: Joel Meyerson <jrm2008 at med.cornell.edu>
> Cc: "chimerax-users at cgl.ucsf.edu" <chimerax-users at cgl.ucsf.edu>
> Subject: [EXTERNAL] Re: [chimerax-users] syntax on marker and marker link placement
>  
>  
> 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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