[chimerax-users] unexpected behavior of build start

[Alexis Rohou]

Thanks Eric!



Sent from a mobile device, with apologies for brevity and typos. 

> On Jul 26, 2021, at 6:21 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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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