[chimerax-users] multiple conformations in one pdb chain

[Eric Pettersen]

Hi Linda,
	Chimera and ChimeraX treat alt locs differently.  Chimera treated them as entirely separate atoms, which meant they naturally all showed at the same time (but which made some chemistry computations much more complicated).  In ChimeraX they are treated as different positions of the same atom, so only the “current” setting/position of the alt loc is shown.  There is no way to show them simultaneously and no easy way to switch between them.  We intend to add some easy interface for switching between them, but we intend to add easy interfaces for many things :-) so it probably will be awhile before that happens.
	Nonetheless, there is a slightly awkward way to switch between alt locs by using the “setattr”  command.  For instance, in the 1a0m PDB entry, this would switch the CB in residue 4 of chain A to the ‘B’ alt loc:

	setattr /a:4 at cb a alt_loc B

which sets the atom-level attribute ‘alt_loc’ for that atom to ‘B’.  That actually changes not only that atom’s alt loc, but possibly also connected atoms in order to make the set of alt locs consistent.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Dec 12, 2019, at 7:16 AM, Linda Schulte <schulte at nmr.uni-frankfurt.de> wrote:
> 
> Hi everyone,
> 
> I have two conformation in a single PDB chain, see example below:
> 
> ATOM  90444  N  APHE z   9     253.604 183.844 259.994  0.50 47.28           N
> ATOM  90455  N  BPHE z   9     253.778 183.499 258.715  0.50 47.28           N
> 
> Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain.
> How can I read in also the B atoms?
> 
> Thanks a lot for your help.
> Best,
> Linda
> 
> 
> 
> -- 
> Linda Schulte
> Goethe-Universität Frankfurt am Main
> Institut für Organische Chemie und Chemische Biologie, AK Schwalbe
> 
> Max-von-Laue-Straße 7
> D-60438 Frankfurt am Main
> N160/300
> 
> +49 (0)69 / 798-29956
> schulte at nmr.uni-frankfurt.de
> 
> 
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