Hi: I am trying to export a scene to obj format. I have tried this export with two different versions of chimera (1.5.3 and 1.6.1), and tried to open the resulting file in two different 3d programs: Cinema 4D and 3d studio max. Although both applications recognize the exported file, when they open it they dont find any content. In C4D, the file is an empty scene, while importer in 3ds max sends an error message telling that there are no objects to import. Therefore, it seems that the file is empty. I have seen that this kind exporting in Chimera is too fast (almost instantly) when compared to exporting to other file formats, like vrml, which take some time but work perfectly. Is there something I am doing wrong or an option I havent noticed to ensure export to obj file format? Thank you in advance, Vicente
Hi Scooter et al, When displaying the surfaces of compound structures (e.g., 1O6K.pdb), surfaces are not displayed in the areas of intermolecular contact. I am using Chimera v 1.6 (build 37500), Mac OSX v10.6.8. We encountered this bug with a previous version, but I don't remember the resolution Image enclosed. Thanks, Peter Hornbeck
Hi Peter, I believe what you are describing is not a bug, it is merely that by default Chimera lumps all the contacting macromolecules into a single enclosed surface. However, you can tell it to enclose sets of atoms separately as you wish. One way is to use the command "split" to make each chain a separate model. Another way (allowing you to retain the whole structure in a single model) is to use "surfcat" to define categories (the groups of atoms you want lumped together) and then "surface" those categories, for example: open 1zik rain chain surfcat achain protein & :.a surfcat bchain protein & :.b surface achain surface bchain I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 4, 2012, at 5:55 AM, Peter Hornbeck wrote:
Hi Scooter et al, When displaying the surfaces of compound structures (e.g., 1O6K.pdb), surfaces are not displayed in the areas of intermolecular contact.
I am using Chimera v 1.6 (build 37500), Mac OSX v10.6.8. We encountered this bug with a previous version, but I don't remember the resolution
Image enclosed.
Thanks, Peter Hornbeck
Hi Peter, Just a P.S.: for your example, the following is sufficient to separate the bound peptide and protein: open 1o6k surfcat peplig protein & :.c This puts the peptide into a surface category named peplig, where the rest of the protein is still in the main surface. The "protein &" part is necessary because chain C also includes waters, but you don't want them included inside the "peplig" surface. Elaine On Jul 4, 2012, at 9:59 AM, Elaine Meng wrote:
Hi Peter, I believe what you are describing is not a bug, it is merely that by default Chimera lumps all the contacting macromolecules into a single enclosed surface. However, you can tell it to enclose sets of atoms separately as you wish.
One way is to use the command "split" to make each chain a separate model.
Another way (allowing you to retain the whole structure in a single model) is to use "surfcat" to define categories (the groups of atoms you want lumped together) and then "surface" those categories, for example:
open 1zik rain chain surfcat achain protein & :.a surfcat bchain protein & :.b surface achain surface bchain
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2012, at 5:55 AM, Peter Hornbeck wrote:
Hi Scooter et al, When displaying the surfaces of compound structures (e.g., 1O6K.pdb), surfaces are not displayed in the areas of intermolecular contact.
I am using Chimera v 1.6 (build 37500), Mac OSX v10.6.8. We encountered this bug with a previous version, but I don't remember the resolution
Image enclosed.
Thanks, Peter Hornbeck
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Hi Vicente, In Chimera 1.6.1 when I use File / Export Scene... and choose file type OBJ the text at the bottom of the dialog says "Only surfaces are exported". Maybe you are expecting molecules to be exported? Tom
Hi:
I am trying to export a scene to obj format. I have tried this export with two different versions of chimera (1.5.3 and 1.6.1), and tried to open the resulting file in two different 3d programs: Cinema 4D and 3d studio max. Although both applications recognize the exported file, when they open it they don’t find any content. In C4D, the file is an empty scene, while importer in 3ds max sends an error message telling that there are no objects to import. Therefore, it seems that the file is empty.
I have seen that this kind exporting in Chimera is too fast (almost instantly) when compared to exporting to other file formats, like vrml, which take some time but work perfectly. Is there something I am doing wrong or an option I haven’t noticed to ensure export to obj file format?
Thank you in advance,
Vicente
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participants (4)
-
Elaine Meng -
Peter Hornbeck -
Tom Goddard -
Vicente Díaz