I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with "chimera file.pdb" the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select "Actions -> Atoms/Bonds -> Show" to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default? Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale@stlcop.edu<mailto:jbeale@stlcop.edu>
Hello John, What I did to configure Chimera on my Linux box was to go into Favorites->Preferences. In the window that opens, choose New Molecules from the drop-down box Category. You can then play with the options there; for what you need, I guess set ribbon display off, atom style as ball, bond style as stick. And maybe also turn off the smart initial display. Hope this helps, Tim On Thu, Aug 12, 2010 at 11:21 AM, Beale, John <John.Beale@stlcop.edu> wrote:
I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with “chimera file.pdb” the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select “Actions -> Atoms/Bonds -> Show” to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default?
Thanks!
John
*John M. Beale, Jr., Ph.D.*
*Professor of Medicinal Chemistry and Pharmacognosy*
*Saint Louis College of Pharmacy*
*4588 Parkview Place*
*Saint Louis, Missouri 63110*
*314-446-8461*
*Cell: 314-315-0409*
*FAX: 314-446-8460*
*jbeale@stlcop.edu*
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Tim is exactly right (thanks!) -- and you do have to turn "smart initial display" to "false" to show all atoms and bonds of subsequently opened structures. Remember to click Save to make the settings apply to later uses of Chimera. Best, 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 Aug 12, 2010, at 8:29 AM, Tim Travers wrote:
Hello John,
What I did to configure Chimera on my Linux box was to go into Favorites->Preferences. In the window that opens, choose New Molecules from the drop-down box Category. You can then play with the options there; for what you need, I guess set ribbon display off, atom style as ball, bond style as stick. And maybe also turn off the smart initial display.
Hope this helps, Tim
On Thu, Aug 12, 2010 at 11:21 AM, Beale, John <John.Beale@stlcop.edu> wrote: <image001.jpg> I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with “chimera file.pdb” the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select “Actions -> Atoms/Bonds -> Show” to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default?
Thanks!
John
John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110
314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460
jbeale@stlcop.edu
_______________________________________________ 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
Hi John, As Tim mentioned, "smart display" off is what you want. Also, "Presets->all atoms" will quickly get you a view of all atoms, though a few of them may be in sphere depiction rather than wireframe. --Eric On Aug 12, 2010, at 8:29 AM, Tim Travers wrote:
Hello John,
What I did to configure Chimera on my Linux box was to go into Favorites->Preferences. In the window that opens, choose New Molecules from the drop-down box Category. You can then play with the options there; for what you need, I guess set ribbon display off, atom style as ball, bond style as stick. And maybe also turn off the smart initial display.
Hope this helps, Tim
On Thu, Aug 12, 2010 at 11:21 AM, Beale, John <John.Beale@stlcop.edu> wrote: <image001.jpg> I have a new installation of Chimera on a Linux box. I am working with a protein/nucleic acid complex. When I start the program with “chimera file.pdb” the ribbon representation of the structure is shown. Also, a plank representation of the nucleic acid is shown. I have to hide the ribbon and select “Actions -> Atoms/Bonds -> Show” to see the atoms. Can someone tell me how to change the startup options so that the ribbon and planks are not automatically generated and that the atoms/bonds are shown by default?
Thanks!
John
John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110
314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460
jbeale@stlcop.edu
_______________________________________________ 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
participants (4)
-
Beale, John -
Elaine Meng -
Eric Pettersen -
Tim Travers