Hello, We are using Chimera to classify viruses. We use pdb files from viper. We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it? Thank you.
I don't understand what you want to do. Here is an example of using the hkcage command http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscag... You will want to add a radius option (e.g. radius 330 for 330 Angstrom radius cage) to that example and you will need to figure out the h and k lattice parameters. Chimera cannot figure out the h,k values you need. I usually try a few values by hand and visually determine the correct values. When you say "shape factor" I guess you probably mean "sphere factor", the Chimera term for the radial interpolation factor (0 to 1) between a flat faced icosahedron and a sphere. Chimera has no way to automatically determine that value. I sometimes judge that by eye using the Icosahedron Surface dialog, menu entry Tools / Higher-Order Structure / Icosahedron Surface That dialog has sliders to adjust the radius of the icosahedron and the "sphere factor" so you can interactively try different values. It would be nice if Chimera could automatically determine the icosahedral coordinate system, outer radius, and best sphere factor, but currently that is only done by eye. Tom
Hello,
We are using Chimera to classify viruses. We use pdb files from viper.
We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it?
Thank you.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Maria, If you mean you want to create a map that is all ones inside a surface, for example inside an icosahedron, I just today made the Chimera "mask" command able to do that. shape icosahedron radius 160 mask ones #0 spacing 3.5 border 20 You would need to get tonight's Chimera daily build to use the "mask ones" capability. Tom
The video has been useful for me, thank you.
Other question: the "meshmol" command creates a molecule model from a surface, there are a command to create a map from a surface?
Thank, María.
-------- Original Message -------- Subject: Re: [Chimera-users] shape factor From: Tom Goddard Date: 5/12/11 9:31 AM
I don't understand what you want to do. Here is an example of using the hkcage command
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscag...
You will want to add a radius option (e.g. radius 330 for 330 Angstrom radius cage) to that example and you will need to figure out the h and k lattice parameters. Chimera cannot figure out the h,k values you need. I usually try a few values by hand and visually determine the correct values. When you say "shape factor" I guess you probably mean "sphere factor", the Chimera term for the radial interpolation factor (0 to 1) between a flat faced icosahedron and a sphere. Chimera has no way to automatically determine that value. I sometimes judge that by eye using the Icosahedron Surface dialog, menu entry
Tools / Higher-Order Structure / Icosahedron Surface
That dialog has sliders to adjust the radius of the icosahedron and the "sphere factor" so you can interactively try different values.
It would be nice if Chimera could automatically determine the icosahedral coordinate system, outer radius, and best sphere factor, but currently that is only done by eye.
Tom
Hello,
We are using Chimera to classify viruses. We use pdb files from viper.
We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it?
Thank you.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Here is a video showing how to display an icosahedral cage for a virus density map using the hkcage command. http://www.cgl.ucsf.edu/chimera/videodoc/cage/ Tom
Hello,
We are using Chimera to classify viruses. We use pdb files from viper.
We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it?
Thank you.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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maznar -
Tom Goddard