[chimerax-users] unexpected behavior of build start

[Eric Pettersen]

Hi Alexis,
	Looking at the "build start atom" code, I can see that it's a bug -- it not adjusting for the fact that the structure's transformation matrix is not the identity matrix.  I will open a ticket in our bug-tracking database for this with you cc'ed.  Should be fixed soon.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jul 26, 2021, at 5:20 PM, Alexis Rohou via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi ChimeraX team,
> 
> I'm running into unexpected behavior when using the build tool.
> 
> Here's what I'm doing:
> - open map --> model #1
> - open PDB --> model #2
> - fit #2 in #1 (the PDB moves by ~20 Å at this step)
> - cofr centerOfView showPivot true
> - move the view around so that the pivot axes intersect where I want to place a new atom
> - build start atom #2
> 
> expected result: a new H atom is created exactly at the center of view (where the pivot axes intersect)
> 
> actual result: the new H atom is created some distance away; I think the vector from where the new H atom is built to the cofr is the same vector as the PDB model was displaced by the fitting into the map (my second step, above), but I haven't checked that carefully. 
> 
> Is this what is expected? It confused me :)
> Is there a command I can use to move the atom to the correct location after it's been created?
> 
> Interestingly, if I add a H atom into a new model, then it appears where I expect it, at the cofr:
> - build start atom "custom built"
> 
> This is with 1.2.5 (2021-05-24)
> 
> Cheers,
> Alexis
> 
> 
> 
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