Hi, I have a molecular dynamics simulation created using Amber, and I visualize the result in Chimera using MD Movie. I would like to show the wandering of a small molecule inside the active site, but in just one picture. Is it possible to include all the positions sampled by some selected atoms in the exported image? Thanks for your help.
Hi David, Not directly, but I know of at least one user who has used a per-frame script with the “define centroid” command to add a ball at the centroid of some residue at each trajectory frame. The resulting figure shows a cloud of balls where that residue has been. See for example Fig 5 in: On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all-Atom Molecular Dynamics Investigation in Water Solution. Pietra F. Chem Biodivers. 2017 Jan;14(1). http://onlinelibrary.wiley.com/doi/10.1002/cbdv.201600158/full You could do that for any set of atoms that can be specified in the command, i.e. it doesn’t have to be a residue. Per-frame scripts in MD Movie: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> The “define” command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> Tutorial with example of per-frame script: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1> The other way would be to play back the trajectory holding the protein as steady as possible and output several separate images (most with only that small molecule) and then composite them in some image-editing app outside of Chimera. You can save images with transparent background. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#transback> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 11:27 AM, David Sáez <davidsaez@udec.cl> wrote:
Hi, I have a molecular dynamics simulation created using Amber, and I visualize the result in Chimera using MD Movie.
I would like to show the wandering of a small molecule inside the active site, but in just one picture. Is it possible to include all the positions sampled by some selected atoms in the exported image?
Thanks for your help.
Dear David, This might be helpful for you, if you have AMBERTOOLS already installed in you machine. If not ignore this suggestion. Pre-process your trajectory file with CPPTRAJ. parm "your ligand name prmtop” trajin “your md trajectory name” start end trajout output.pdb pdb append eg. parm test.parm7 trajin test.mdcrd 1 10 trajout output.pdb pdb append and then load all the merged ligand PDBs in CHIMERA. David
On Jul 16, 2018, at 11:52 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi David, Not directly, but I know of at least one user who has used a per-frame script with the “define centroid” command to add a ball at the centroid of some residue at each trajectory frame. The resulting figure shows a cloud of balls where that residue has been.
See for example Fig 5 in: On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all-Atom Molecular Dynamics Investigation in Water Solution. Pietra F. Chem Biodivers. 2017 Jan;14(1). http://onlinelibrary.wiley.com/doi/10.1002/cbdv.201600158/full
You could do that for any set of atoms that can be specified in the command, i.e. it doesn’t have to be a residue.
Per-frame scripts in MD Movie: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> The “define” command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> Tutorial with example of per-frame script: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part1>
The other way would be to play back the trajectory holding the protein as steady as possible and output several separate images (most with only that small molecule) and then composite them in some image-editing app outside of Chimera. You can save images with transparent background. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#transback>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2018, at 11:27 AM, David Sáez <davidsaez@udec.cl> wrote:
Hi, I have a molecular dynamics simulation created using Amber, and I visualize the result in Chimera using MD Movie.
I would like to show the wandering of a small molecule inside the active site, but in just one picture. Is it possible to include all the positions sampled by some selected atoms in the exported image?
Thanks for your help.
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participants (3)
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David Gae -
David Sáez -
Elaine Meng