Can you morph a ligand
Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question: We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well? Thanks, Walt -- Walter Fast, Ph.D. Associate Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast@mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html
Hi Walt, Thanks for the compliments -- and (even without the compliments) nice to hear from you! The morph trajectory will only include the atoms that are in both input conformations. They would have to be recognized as "atoms in common" in order to be retained. I was going to say that perhaps this could be done with tricky renaming if the numbers of atoms were the same, but on second thought, that may not work. I haven't tried it. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
However, you can certainly still display those unique parts from the input models along with the trajectory, they just won't morph. Morphing with "hide conformations" turns off the model display of the input structures. You could turn them back on with the "modeldisplay" command or by checking the "Shown" boxes in the Model Panel. You would probably want to ~ribbon, ~disp the other parts of those input structures. Say your input structures were models 0 and 1 and the morph trajectory is model 2. To show (for example) the ligand and ions from model 1 you could use the commands: modeldisp #1 ~ribbon #1 ~disp #1 disp #1 & ligand disp #1 & ions In MD Movie, the tool that shows the morph trajectory, you could script it so that these atoms would appear at a certain frame. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#pe...
If you are displaying ribbons, another thing you may want to include in a per-frame script is re-evaluating the secondary structure at each frame with the "ksdssp" command. For default settings the command would simply be "ksdssp" without arguments. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> Other than using the MD Movie dialog, another option for playing back the trajectory is the "coordset" command. This is not integrated with the scripting in the MD Movie dialog, however. Basically the same things could be done, just in a different way, possibly with some combination of the "coordset" and "perframe" commands: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 9, 2009, at 11:50 AM, Walter Fast wrote:
Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question:
We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well?
Thanks, Walt
Thanks Elaine, we'll give it a try. For teaching, this Friday I'll use Chimera in lecture with red/cyan glasses for everyone - from my view it looks just like an old 50s 3D movie audience! You are always so helpful - Thanks! Best, Walt -- Walter Fast, Ph.D. Associate Professor The University of Texas at Austin College of Pharmacy The Division of Medicinal Chemistry Phone: (512) 232-4000 Fax: (512) 232-2606 Lab: (512) 471-5839 Email: WaltFast@mail.utexas.edu http://www.utexas.edu/pharmacy/divisions/medicinalchem/faculty/fast.html On 9/9/09 2:47 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Walt, Thanks for the compliments -- and (even without the compliments) nice to hear from you!
The morph trajectory will only include the atoms that are in both input conformations. They would have to be recognized as "atoms in common" in order to be retained. I was going to say that perhaps this could be done with tricky renaming if the numbers of atoms were the same, but on second thought, that may not work. I haven't tried it. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
However, you can certainly still display those unique parts from the input models along with the trajectory, they just won't morph. Morphing with "hide conformations" turns off the model display of the input structures. You could turn them back on with the "modeldisplay" command or by checking the "Shown" boxes in the Model Panel. You would probably want to ~ribbon, ~disp the other parts of those input structures.
Say your input structures were models 0 and 1 and the morph trajectory is model 2. To show (for example) the ligand and ions from model 1 you could use the commands:
modeldisp #1 ~ribbon #1 ~disp #1 disp #1 & ligand disp #1 & ions
In MD Movie, the tool that shows the morph trajectory, you could script it so that these atoms would appear at a certain frame. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#pe... -frame
If you are displaying ribbons, another thing you may want to include in a per-frame script is re-evaluating the secondary structure at each frame with the "ksdssp" command. For default settings the command would simply be "ksdssp" without arguments. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
Other than using the MD Movie dialog, another option for playing back the trajectory is the "coordset" command. This is not integrated with the scripting in the MD Movie dialog, however. Basically the same things could be done, just in a different way, possibly with some combination of the "coordset" and "perframe" commands: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 9, 2009, at 11:50 AM, Walter Fast wrote:
Hi! Chimera is great - thanks again! I use it all the time for research and teaching. I have a quick question:
We have two different product-bound structures, but when I morph between the two we loose the active site metal ions and the active-site ligands. Is there a way to include these as well?
Thanks, Walt
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Elaine Meng -
Walter Fast