[Chimera-users] Setting a pathway/trajectory for a molecule

[Rani Wiswedel]

Hi Elaine,

Apologies for the confusion, this helps a great deal thank you!
I think option 1 will work very well.

Kind regards,
Rani

On Fri, Sep 18, 2020 at 11:35 PM Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:
Hi Rani,
Ah.... asking questions is actually a skill equal to answering questions!

I don't really know what "set up the pathway" means, i.e. what you need to carry out the later steps of your calculation.  I can think of a few general approaches.

(1) Place single dots or balls along the path. These would essentially be fake or dummy atoms (aka markers), and Volume Tracer is one of the ways to add them, but the difficult part is how to put them where you want them.  Since you aren't marking a volume (something like a density map), it will be hard to control the depth of placement and you would have to spend a fair amount of time dragging the individual markers to the middle of the pore.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

If the pore protein is symmetrical, maybe you could instead use the "measure center" command with the option "mark true" several times to calculate the centroids for rings of atoms along the length of the pore and add them as as markers.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>

(2) Manually place the whole substrate in the pore in different positions along the path, and save it in these different positions.

To do this, you would need to open the protein and the substrate from two separate files so that they are two separate models in Chimera.  Then you could do the manual placement with the mouse, freezing/unfreezing one model or the other so that you can move them separately.  Details:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

Then use menu: File... Save PDB and save just the substrate model but "relative to" the pore model.  Then move it along the path a bit and save it again.  You would do this several times to save different PDB files containing the different positions of the substrate along the path.  When you save "relative to" that means if you open the original pore-model file, all the newly saved substrate files will be in the correct positions relative to the pore.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

(3) Or, perhaps there is a hybrid approach where you do it like method (2) but instead of the whole substrate you just open a PDB file that contains only one atom.  It depends how many of those you need to place as to how tedious the overall process would be. if you wanted the path in a single file, you could open all the saved positions simultaneously and then either save them to a single multi-model PDB, or combine into a single model (e.g. with "combine" command)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
and then save that new single model PDB file.

Good luck with your project,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 18, 2020, at 1:38 PM, Rani Wiswedel <wswran001 at myuct.ac.za<mailto:wswran001 at myuct.ac.za>> wrote:
>
> Hi Elaine
>
> Thank you very much for your quick reply. I don't think I will be running the actual simulations on Chimera, I was just told to set up the pathway of the substrate through the pore; specify points that would create a pathway for the substrate to travel through the pore structure. Would this be possible?
>
> I also looked at the Volume Path Tracer, but this doesn't seem to be appropriate either?
>
> Thank you again
>
> Regards,
> Rani
>
>
> On Fri, 18 Sep 2020, 22:26 Elaine Meng, <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:
> Hi Rani,
> Chimera is not the right program to do something like this.  Please see the discussion from earlier today, shown in these links:
>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017228.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017234.html>
>
> As mentioned in those posts, it is not appropriate for larger systems or when long simulations are needed.  Also it does not have any options for guiding sampling along a path or for calculating free energies.  Some other programs you might consider for running molecular dynamics calculations are given in those posts.
>
> That tutorial you mention is not about running any molecular dynamics simulation.  It only gives an example of looking at molecular dynamics results that were saved from another program (AMBER) that actually did the calculations.
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Sep 18, 2020, at 12:56 PM, Rani Wiswedel <wswran001 at myuct.ac.za<mailto:wswran001 at myuct.ac.za>> wrote:
> >
> > Good day,
> > I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do?
> > Any advice would be greatly appreciated, I am in way over my depth.
> > Thank you
> > Kind regards,
> > Rani
> >

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