I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?
Hi Erin, If you rotate or move the surface with the mouse in Chimera before exporting it then the rotated and moved position will be saved. So if you want the OBJ to align with the PDB file when loaded in other software you should make sure you don't rotate or move the surface or molecule in Chimera. If you do rotate or move the surface you can put them back in their original unrotated unmoved position with the Chimera commad "reset" (menu Favorites / Command-line). Tom
On Nov 6, 2015, at 10:01 AM, Erin Cutts wrote:
I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?
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Yeah, that got it, works wonderfully now! I thought the translations all looked pretty random, as random as a lunatic with a mouse. ________________________________ From: Tom Goddard [goddard@sonic.net] Sent: 06 November 2015 21:12 To: Erin Cutts Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] obj file origin Hi Erin, If you rotate or move the surface with the mouse in Chimera before exporting it then the rotated and moved position will be saved. So if you want the OBJ to align with the PDB file when loaded in other software you should make sure you don't rotate or move the surface or molecule in Chimera. If you do rotate or move the surface you can put them back in their original unrotated unmoved position with the Chimera commad "reset" (menu Favorites / Command-line). Tom On Nov 6, 2015, at 10:01 AM, Erin Cutts wrote: I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space? _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edumailto:Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Erin Cutts -
Tom Goddard