[chimerax-users] distance between centers of mass using python API

[Eric Pettersen]

We are thinking it would be nice if the marker atom also got the given name so that you could use:

	dist @AA1 @AA2

And will probably make that enhancement today, so it will be in tomorrow's daily build.

--Eric

> On Sep 7, 2021, at 11:20 AM, Eric Pettersen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Diego,
> 	Centroids are created as 'markers' and therefore are referred to in commands in the same way as atoms are.  So specifically, your first 'define' command creates a structure named AA1, with one residue named 'centroid', with one atom named 'cent'.  Therefore this command will create the distance:
> 
> 	dist ##name=AA1 ##name=AA2
> 
> If you have exactly two of these centroids open, then this command will also do it:
> 
> 	dist :centroid
> 
> Therefore, it might be easiest to not even give these centroids names but instead use two 'define' commands followed by 'dist :centroid' and then 'close :centroid'.
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Sep 6, 2021, at 10:14 AM, Diego Amaya via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> Hello,
>> 
>> I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways :
>> 
>> 1. 
>> rc(session, 'define centroid :43 massWeighting  true name AA1')
>> rc(session, 'define centroid :35 massWeighting  true name AA2')
>> rc(session, 'distance AA1 AA2')
>> 
>> 2.
>> rc(session, ' measure center :43 mark true name AA1')
>> rc(session, 'measure center :35 mark true name AA2')
>> rc(session, 'distance AA1 AA2')
>> 
>> But I get this error in the third line in both cases : 
>> chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier 
>> 
>> What is wrong ?
>> 
>> Thanks in advance.
>> -- 
>> Diego A. Amaya Ramírez
>> 
>> Aviso legal: El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>. Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210907/9428d4dd/attachment.html>