On May 25, 2010, at 10:39 PM, 江一波 wrote:
hello meng! how can i construct a virus by chimera? i have get a nucleocapsid protein about a virus from http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! i want construct a virus ...how can i do? is there somethings paper about how to construct ? thank you!!!
Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file. Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found. Sorry, I don't have any ideas about how to make a whole capsid from this structure. A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid. Please send Chimera questions to the chimera-users@cgl.ucsf.edu address. Thanks, Elaine ------------------------------ Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Although PDB 2i9f is a virus nucleocapsid protein the crystal did not contain whole or partial capsids so the capsid organization was not determined from the crystallography. How do I know that? I displayed the unit cell using the "Make Copies" button in the Unit Cell dialog (menu Tools / Higher-Order Structure). There are 8 copies in the unit cell in a clearly non-capsid arrangement. I do not know if there is other experimental data which determines the capsid arrangement for this virus. Would need to look at the associated journal article. Tom
On May 25, 2010, at 10:39 PM, 江一波 wrote:
hello meng! how can i construct a virus by chimera? i have get a _nucleocapsid protein _ about a virus from http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current <http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current> such as ,i get ID :2I9F <http://www.rcsb.org/pdb/explore/explore.do?structureId=2I9F> structure...one of a nucleocapsid for a virus ...this is symmetrical structure! i want construct a virus ...how can i do? is there somethings paper about how to construct ? thank you!!!
Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file.
Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found.
Sorry, I don't have any ideas about how to make a whole capsid from this structure.
A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid.
Please send Chimera questions to the chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> address. Thanks, Elaine ------------------------------ Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
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I think the problem here is that the capsid of equine arterivirus is most likely not icosahedral... Terje Dokland's group performed cryo-electron tomography on the related arterivirus PRRSV (PMID 19218197). Those data showed no evidence of an icosahedral core. D. On 27 May 2010, at 00:30, Tom Goddard wrote: Although PDB 2i9f is a virus nucleocapsid protein the crystal did not contain whole or partial capsids so the capsid organization was not determined from the crystallography. How do I know that? I displayed the unit cell using the "Make Copies" button in the Unit Cell dialog (menu Tools / Higher-Order Structure). There are 8 copies in the unit cell in a clearly non-capsid arrangement. I do not know if there is other experimental data which determines the capsid arrangement for this virus. Would need to look at the associated journal article. Tom
On May 25, 2010, at 10:39 PM, 江一波 wrote:
hello meng! how can i construct a virus by chimera? i have get a nucleocapsid protein about a virus from http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtoshow=Current such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! i want construct a virus ...how can i do? is there somethings paper about how to construct ? thank you!!!
Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file.
Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found.
Sorry, I don't have any ideas about how to make a whole capsid from this structure.
A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid.
Please send Chimera questions to the chimera-users@cgl.ucsf.edu address. Thanks, Elaine ------------------------------ Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
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_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users Dr David Bhella MRC Virology Unit Church Street Glasgow G11 5JR Telephone: 0141-330-3685 Graphics lab: 0141-330-2989 Skype: d.bhella Virus Structure Web Site: http://www.mrcvu.gla.ac.uk/research/bhellad/virus_structure.htm Molecular Machines - Images from Virus Research (Art Exhibition): http://www.molecularmachines.org.uk Departmental Web Site: http://www.mrcvu.gla.ac.uk/staff/bhellad.html
participants (3)
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David Bhella -
Elaine Meng -
Tom Goddard