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
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@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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Thanks Eric! Sent from a mobile device, with apologies for brevity and typos.
On Jul 26, 2021, at 6:21 PM, Eric Pettersen <pett@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@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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participants (2)
-
Alexis Rohou -
Eric Pettersen