Command to select atoms of pseudobonds

[meng@…]

Want a command like "select atoms pbonds" that selects the atom endpoints of pseudobonds.

Begin forwarded message:

From: Elaine Meng
Subject: how to select pbond end atoms in ChimeraX?
Date: January 2, 2018 at 1:53:04 PM PST
To: Eric Pettersen
Cc: Tom Goddard

Maybe I’m having a brain glitch, but now that “hbonds” and “pbonds” specify just the pseudobonds themselves, I can’t think of an easy way to specify (or select) their endpoint atoms. I guess we could add a “select” option to the hbonds command at the time of H-bond detection (analogous to the option already in “contacts”) but we should have a way to do it after the fact too, for example to select all atoms involved in hbonds from an mmCIF file.

...

Elaine

[Tom Goddard]

I added an "hbondatoms" selector that specifies the endpoint atoms of the bonds given by the hbonds selector to handle the most common need.

Eric points out that we should handle more general uses too.

Begin forwarded message:

From: Eric Pettersen <pett@…>
Subject: Re: how to select pbond end atoms in ChimeraX?
Date: January 5, 2018 at 2:41:39 PM PST
To: Tom Goddard
Cc: Elaine Meng

On Jan 2, 2018, at 2:06 PM, Tom Goddard wrote:

Hi Elaine,

I think there is no way to specify endpoint atoms starting with pbonds or hbonds specifiers. I ran into this a month ago. It is an uncommon need. Maybe we could add “select atoms pbonds”. Maybe we just add selectors pbondatoms and hbondatoms.

Tom

While the latter is fine as a stopgap (and is what you implemented), I think we need something like the former so that extensions that create their own pseudobonds (e.g. crosslinks or NMR constraints) don’t need to also create their own selectors. Maybe an RFE ticket should be created?

—Eric