Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu
Hi Kevin, I tried coloring PDB 1a0m surface (Actions / Surface / show) by bfactor, saving a session, restarting, opening session, and the colors were correctly restored in Chimera versions 1.3 and 1.4 (daily build). Maybe you are using an older Chimera? Chimera menu Help / About UCSF Chimera will tell you the version. Another possibility is that you are display some other kind of surface (e.g. a density map isosurface) where the coloring is not recorded in the session. Tom Kevin Wu wrote:
Hi all,
I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data?
Thanks in advance! Kevin Wu
------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Thomas, The colors do correctly restore, but if the render by attribute window is opened again, the data about the color doesn't seem to be saved. I cannot modify the colors or values. Thanks! Kevin On May 18, 2009, at 11:53, Thomas Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Kevin,
I tried coloring PDB 1a0m surface (Actions / Surface / show) by bfactor, saving a session, restarting, opening session, and the colors were correctly restored in Chimera versions 1.3 and 1.4 (daily build). Maybe you are using an older Chimera? Chimera menu Help / About UCSF Chimera will tell you the version. Another possibility is that you are display some other kind of surface (e.g. a density map isosurface) where the coloring is not recorded in the session.
Tom
Kevin Wu wrote:
Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu --- --------------------------------------------------------------------- _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kevin, Yes, the settings that produced the surface coloring using Render by Attribute are not saved in the session, only the coloring is. I agree that the settings should be saved. Eric Pettersen wrote the Render by Attribute code and can comment on whether this will happen in the future. Tom Kevin Wu wrote:
Hi Thomas,
The colors do correctly restore, but if the render by attribute window is opened again, the data about the color doesn't seem to be saved. I cannot modify the colors or values.
Thanks! Kevin
On May 18, 2009, at 11:53, Thomas Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Kevin,
I tried coloring PDB 1a0m surface (Actions / Surface / show) by bfactor, saving a session, restarting, opening session, and the colors were correctly restored in Chimera versions 1.3 and 1.4 (daily build). Maybe you are using an older Chimera? Chimera menu Help / About UCSF Chimera will tell you the version. Another possibility is that you are display some other kind of surface (e.g. a density map isosurface) where the coloring is not recorded in the session.
Tom
Kevin Wu wrote:
Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu ------------------------------------------------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kevin, You are right that the Render by Attribute doesn't save it's state in sessions. You should nonetheless be able to recolor your surface using that tool, though you will have to start from the default values rather than the values of the session. I will open an enhancement request in our Trac database for this session-saving feature with you on the recipient list, so you will know when it gets implemented. It will take a while because there are a lot of high-value features ahead of it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 18, 2009, at 1:10 PM, Thomas Goddard wrote:
Hi Kevin,
Yes, the settings that produced the surface coloring using Render by Attribute are not saved in the session, only the coloring is. I agree that the settings should be saved. Eric Pettersen wrote the Render by Attribute code and can comment on whether this will happen in the future.
Tom
Kevin Wu wrote:
Hi Thomas,
The colors do correctly restore, but if the render by attribute window is opened again, the data about the color doesn't seem to be saved. I cannot modify the colors or values.
Thanks! Kevin
On May 18, 2009, at 11:53, Thomas Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Kevin,
I tried coloring PDB 1a0m surface (Actions / Surface / show) by bfactor, saving a session, restarting, opening session, and the colors were correctly restored in Chimera versions 1.3 and 1.4 (daily build). Maybe you are using an older Chimera? Chimera menu Help / About UCSF Chimera will tell you the version. Another possibility is that you are display some other kind of surface (e.g. a density map isosurface) where the coloring is not recorded in the session.
Tom
Kevin Wu wrote:
Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu ------------------------------------------------------------------------ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Eric Pettersen -
Kevin Wu -
Kevin Wu -
Thomas Goddard