Hello ChimeraX Users, I'm trying to make a movie in chimerax involving a membrane protein, and I would like to have some representation of where the inner and outer lipid bilayer leaflets are relative to the protein transmembrane region, ideally represented as phospholipids. Is it possible to do this within Chimerax? I've thought about encoding the movie to mp4 and then figuring out how to simply overlay a bilayer image onto the mp4 where I want with some other software , but I foresee resolution and scaling issues when doing that. Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University
Hi Kevin, If a simplified representation might be acceptable, I'd first look at the OPM database (orientations of proteins in membranes) which has versions of PDB entries with planar arrays of pseudoatoms representing the predicted inner and outer hydrophobic membrane boundaries. I made an example image and script (.cxc file linked to the explanation) in which I used "define plane" in ChimeraX to make semitransparent discs from the OPM pseudoatoms. Coincidentally it is the featured image on our homepage today: <https://www.rbvi.ucsf.edu/chimerax/index.html> ...but its more constant location is here: <https://www.rbvi.ucsf.edu/chimerax/features.html#axesplanes> I'd done a similar thing in Chimera: <https://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopa...> Of course, that is just for a single static structure, and if the one you want isn't in OPM, you'd need to get a similar entry and then superimpose it with your structure and then hide that protein, leaving just the "membrane" together with your own protein. Also if you disagree with the predicted location, I suppose you could just move the discs to whever you think the membrane boundary should be, so perhaps it wouldn't even need to be an OPM entry of a homolog, just something of similar size. If you need an actual atomic membrane, I think there are web servers to create them, but I haven't used any of them myself, and I can't recall specific names. I had a couple of bookmarks saved in my browser but most are obsolete (the URLs no longer work). The only one I can find currently is Memgen, but again, I've never tried it myself, so caveat emptor: <https://memgen.uni-saarland.de/#/memgen> According to the Memgen help, it doesn't put proteins into the bilayer, you have to do it separately and delete the molecules that intersect with the protein. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 20, 2024, at 2:44 PM, Kevin Felt via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Users,
I'm trying to make a movie in chimerax involving a membrane protein, and I would like to have some representation of where the inner and outer lipid bilayer leaflets are relative to the protein transmembrane region, ideally represented as phospholipids. Is it possible to do this within Chimerax? I've thought about encoding the movie to mp4 and then figuring out how to simply overlay a bilayer image onto the mp4 where I want with some other software , but I foresee resolution and scaling issues when doing that. Thank you!
Sincerely,
-- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University
Thank you so much Dr. Meng, worked like a charm! Sincerely, On Wed, Mar 20, 2024 at 7:40 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kevin, If a simplified representation might be acceptable, I'd first look at the OPM database (orientations of proteins in membranes) which has versions of PDB entries with planar arrays of pseudoatoms representing the predicted inner and outer hydrophobic membrane boundaries.
I made an example image and script (.cxc file linked to the explanation) in which I used "define plane" in ChimeraX to make semitransparent discs from the OPM pseudoatoms.
Coincidentally it is the featured image on our homepage today: <https://www.rbvi.ucsf.edu/chimerax/index.html> ...but its more constant location is here: <https://www.rbvi.ucsf.edu/chimerax/features.html#axesplanes>
I'd done a similar thing in Chimera: < https://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopa...
Of course, that is just for a single static structure, and if the one you want isn't in OPM, you'd need to get a similar entry and then superimpose it with your structure and then hide that protein, leaving just the "membrane" together with your own protein. Also if you disagree with the predicted location, I suppose you could just move the discs to whever you think the membrane boundary should be, so perhaps it wouldn't even need to be an OPM entry of a homolog, just something of similar size.
If you need an actual atomic membrane, I think there are web servers to create them, but I haven't used any of them myself, and I can't recall specific names. I had a couple of bookmarks saved in my browser but most are obsolete (the URLs no longer work). The only one I can find currently is Memgen, but again, I've never tried it myself, so caveat emptor:
<https://memgen.uni-saarland.de/#/memgen>
According to the Memgen help, it doesn't put proteins into the bilayer, you have to do it separately and delete the molecules that intersect with the protein.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 20, 2024, at 2:44 PM, Kevin Felt via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello ChimeraX Users,
I'm trying to make a movie in chimerax involving a membrane protein, and I would like to have some representation of where the inner and outer lipid bilayer leaflets are relative to the protein transmembrane region, ideally represented as phospholipids. Is it possible to do this within Chimerax? I've thought about encoding the movie to mp4 and then figuring out how to simply overlay a bilayer image onto the mp4 where I want with some other software , but I foresee resolution and scaling issues when doing that. Thank you!
Sincerely,
-- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University
-- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University
participants (2)
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Elaine Meng -
Kevin Felt