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

[Joel Meyerson]

Hi Tom,
I used a simple workaround by creating the markers separately based on alpha-carbon position, getting each of their x,y,z coordinates, creating a new pair of markers using the coordinates, and then drawing the line between the new markers.

Thanks,
Joel

From: Tom Goddard <goddard at sonic.net>
Date: Saturday, April 11, 2020 at 5:25 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

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<mailto: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<mailto:goddard at sonic.net>>
Date: Saturday, April 11, 2020 at 4:41 PM
To: Joel Meyerson <jrm2008 at med.cornell.edu<mailto:jrm2008 at med.cornell.edu>>
Cc: "chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>" <chimerax-users at cgl.ucsf.edu<mailto: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
_______________________________________________
ChimeraX-users mailing list
ChimeraX-users at cgl.ucsf.edu<mailto:ChimeraX-users at cgl.ucsf.edu>
Manage subscription:
http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=fzZblJRz4mXN2MmDMiN5zccNMmjMAHuZXC-PM7zbX-Q&s=EnyBgOSNOVHTtyTXzIch74ammVljsIkLkmF1uSqvIP8&e=>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200412/ea823cc2/attachment-0001.html>