Proposal to an add on
Hello, I hope everyone is doing well. I know I have asked this before about the molmaps and have been trying to work around the "holes", in order to create a solid map for the inner volume calculation. It works very well with the AAVs, however with the other subfamilies because of their larger pores it makes it to where it is an inconsistent volume contour, and I believe it throws off the inner volume calculations. I propose to add an element to only cover the pores as a means to make the contour thinner to create a more realistic inner volume calculation. I would like to help with this feature, as my skills have improved within the last year since I first started using Chimera and ChimeraX for my project. I am unsure how I go about this and your response. I have reached out before and most of the time it ends in maybe trying another software. There is no other software that is remotely comparable to this molmap feature that is as user-friendly as it is in ChimeraX. I would really like to continue the use of ChimeraX. I have also thought of possibly trying to create a way for the molecular surface to work with the volume blob feature, but it still comes down to the pores creating the holes. A mechanism to create a feature of only covering the pores could be useful for not only my project but others that may have similar issues. Please let me know what your thoughts are as I would like to contribute to this resolution, but would also need some direction on how to start it. Thank you and I hope to hear from you soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Hi Heather, The problem is that Chimera and ChimeraX do not really have a way to measure the size of a pocket that has any openings. I'm guessing that other programs have solved this problem, but I do not have a list off the top of my head, nor have I tried them, nor do I know if they work on something on the scale of a viral capsid. Maybe others on this list have suggestions of what other program(s) to try? The only one I've used is CASTp, but that is generally for something like a single protein (enzyme or receptor). I don't know if you could run it on a large assembly or not. <http://sts.bioe.uic.edu/castp/index.html?2cpk> <http://sts.bioe.uic.edu/castp/calculation.html> My only idea in Chimera/ChimeraX is to create an idealized sphere or icosahedron shape of the largest size that nests within the inner surface of your capsid (determined iteratively by eye), and then calculate the volume of idealized sphere or icosahedron. The idealized surface could be created with "shape" and measured with "measure volume" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume> Another way to draw a sphere shape is with the Volume Eraser tool, e.g. in ChimeraX, click "Right Mouse" in the toolbar tab across the top and then the icon that looks like a surface with a pink sphere on it. Then you get a Map Eraser dialog that has a slider for radius, which may be easier than using "shape sphere" or "shape icosahedron" repeatedly, and you can drag the sphere around to reposition using the right mouse (= trackpad + Alt on Windows, trackpad + command key on Mac) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 31, 2022, at 6:28 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I hope everyone is doing well. I know I have asked this before about the molmaps and have been trying to work around the "holes", in order to create a solid map for the inner volume calculation. It works very well with the AAVs, however with the other subfamilies because of their larger pores it makes it to where it is an inconsistent volume contour, and I believe it throws off the inner volume calculations. I propose to add an element to only cover the pores as a means to make the contour thinner to create a more realistic inner volume calculation. I would like to help with this feature, as my skills have improved within the last year since I first started using Chimera and ChimeraX for my project. I am unsure how I go about this and your response.
I have reached out before and most of the time it ends in maybe trying another software. There is no other software that is remotely comparable to this molmap feature that is as user-friendly as it is in ChimeraX. I would really like to continue the use of ChimeraX. I have also thought of possibly trying to create a way for the molecular surface to work with the volume blob feature, but it still comes down to the pores creating the holes. A mechanism to create a feature of only covering the pores could be useful for not only my project but others that may have similar issues. Please let me know what your thoughts are as I would like to contribute to this resolution, but would also need some direction on how to start it. Thank you and I hope to hear from you soon.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Heather, Here's an idea for plugging the virus capsid holes so you can measure the interior volume. Make an icosahedron surface that blocks the holes, then increase the virus capsid density map values outside the icosahedron so the density is solid (no holes at your threshold level of interest). Then you could subtract the volume inside the modified density map from the volume of the cube to get the interior volume. Here are some commands and images showing the idea. First make the capsid map from the atomic model. open 7ns0 sym #1 assembly 1 copies true molmap #2 8 Then make an icosahedron shape to plug the holes shape icos radius 160 center #2 orient n25r sphere .5 color yellow Then make a mask outside the icosahedron volume onesmask #4 invert true ongrid #3 Then scale and add that mask to the original volume volume scale #5 factor 10 volume add #3,6 Then measure the volume enclosed by the map surface and the volume in the map cube (by lowering the threshold to less than the lowest density), then subtract measure volume #7 > Enclosed volume for surface (#6.1) = 5.149e+07 volume #7 level -100 measure volume #7 Enclosed volume for surface (#6.1) = 6.224e+07 Interior volume = 1.075e7 cubic Angstroms (= 6.224e7 - 5.149e7). Comparing to the volume inside the icosahedron measure volume #4 > Enclosed volume for icosahedron (#4) = 1.345e+07 it makes sense that the virus interior is a bit smaller. Tom Capsid map, icosahedron, map holes blocked by icosahedron, mask outside icosahedron, capsid map with density increased outside icosahedron. Some images shown clipped in half for clarity.
On Aug 31, 2022, at 6:28 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I hope everyone is doing well. I know I have asked this before about the molmaps and have been trying to work around the "holes", in order to create a solid map for the inner volume calculation. It works very well with the AAVs, however with the other subfamilies because of their larger pores it makes it to where it is an inconsistent volume contour, and I believe it throws off the inner volume calculations. I propose to add an element to only cover the pores as a means to make the contour thinner to create a more realistic inner volume calculation. I would like to help with this feature, as my skills have improved within the last year since I first started using Chimera and ChimeraX for my project. I am unsure how I go about this and your response.
I have reached out before and most of the time it ends in maybe trying another software. There is no other software that is remotely comparable to this molmap feature that is as user-friendly as it is in ChimeraX. I would really like to continue the use of ChimeraX. I have also thought of possibly trying to create a way for the molecular surface to work with the volume blob feature, but it still comes down to the pores creating the holes. A mechanism to create a feature of only covering the pores could be useful for not only my project but others that may have similar issues. Please let me know what your thoughts are as I would like to contribute to this resolution, but would also need some direction on how to start it. Thank you and I hope to hear from you soon.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Noriega, Heather -
Tom Goddard