moving map with model in chimerax
Dear experts, I am preparing figures for a paper, and I would like to color several structures using apbs dx maps. I manage todo that, but I need to move or align the coordinates of the pdb in order to map several different maps, and when I save the chimerax session and reopen, the map is not aligned with the new coordinates of the pdb, so the colouring fails. So is there a way to move or associate the map with a certain model, and move it together with it? Tahnks a lot, Fabian ---------------------------------------------------------------------------- Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701
Hi Fabian! If the dx map and the atomic structure (pdb) are aligned when you first open them, but then you move only the atomic structure, you can later apply the same transformation to the map using the "view position" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position> For example, if the atomic structure is #1 and the dx map that goes with it is #2, but you moved only #1, then to also move the map to realign them, command: view position #2 sameas #1 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2021, at 5:27 AM, Fabian Glaser <fabian.glaser@gmail.com> wrote:
Dear experts, I am preparing figures for a paper, and I would like to color several structures using apbs dx maps. I manage todo that, but I need to move or align the coordinates of the pdb in order to map several different maps, and when I save the chimerax session and reopen, the map is not aligned with the new coordinates of the pdb, so the colouring fails.
So is there a way to move or associate the map with a certain model, and move it together with it? Tahnks a lot, Fabian
Dear Elaine, Thanks a lot! It solved my problem. Best regards, Fabian
On 20 May 2021, at 20:32, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Fabian!
If the dx map and the atomic structure (pdb) are aligned when you first open them, but then you move only the atomic structure, you can later apply the same transformation to the map using the "view position" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>
For example, if the atomic structure is #1 and the dx map that goes with it is #2, but you moved only #1, then to also move the map to realign them, command:
view position #2 sameas #1
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2021, at 5:27 AM, Fabian Glaser <fabian.glaser@gmail.com> wrote:
Dear experts, I am preparing figures for a paper, and I would like to color several structures using apbs dx maps. I manage todo that, but I need to move or align the coordinates of the pdb in order to map several different maps, and when I save the chimerax session and reopen, the map is not aligned with the new coordinates of the pdb, so the colouring fails.
So is there a way to move or associate the map with a certain model, and move it together with it? Tahnks a lot, Fabian
participants (2)
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Elaine Meng -
Fabian Glaser