Aligning a 2Fo-Fc map with the molecule in Chimera
The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error: NameError: global name 'step' is not defined File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False) Hoping to figure out how to make it work. Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin@tu.edu mgochin@lbl.gov 707-638-5463
Hi Miriam, We appreciate your long use of Chimera! That bug was fixed 7 years ago. Time to install a new Chimera. Tom
On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin@lbl.gov> wrote:
The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error:
NameError: global name 'step' is not defined
File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
Hoping to figure out how to make it work.
Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin@tu.edu <mailto:miriam.gochin@tu.edu> mgochin@lbl.gov <mailto:mgochin@lbl.gov> 707-638-5463 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks for date shaming me!! It works - you guys are great. Is there any way to select certain parts of the map, if for example you just want to see the electron density of one molecule instead of all the symmetry copies? Miriam PS. 7 years isn't even close. On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Miriam,
We appreciate your long use of Chimera! That bug was fixed 7 years ago. Time to install a new Chimera.
Tom
On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin@lbl.gov> wrote:
The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error:
NameError: global name 'step' is not defined
File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
Hoping to figure out how to make it work.
Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin@tu.edu mgochin@lbl.gov 707-638-5463 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Miriam, Sorry! To show the map just near the atoms use Volume Viewer menu Features / Zone, select your atoms (e.g. command "select #0") and press the Zone button. This just hides the density beyond some distance (e.g. 3 Angstroms) from the selected atoms. Tom
On Feb 20, 2020, at 1:26 PM, Miriam Gochin <mgochin@lbl.gov> wrote:
Thanks for date shaming me!! It works - you guys are great. Is there any way to select certain parts of the map, if for example you just want to see the electron density of one molecule instead of all the symmetry copies?
Miriam
PS. 7 years isn't even close.
On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote: Hi Miriam,
We appreciate your long use of Chimera! That bug was fixed 7 years ago. Time to install a new Chimera.
Tom
On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin@lbl.gov <mailto:mgochin@lbl.gov>> wrote:
The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error:
NameError: global name 'step' is not defined
File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
Hoping to figure out how to make it work.
Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin@tu.edu <mailto:miriam.gochin@tu.edu> mgochin@lbl.gov <mailto:mgochin@lbl.gov> 707-638-5463 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Thank you so much for your help. Works great. On Thu, Feb 20, 2020 at 1:37 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Miriam,
Sorry! To show the map just near the atoms use Volume Viewer menu Features / Zone, select your atoms (e.g. command "select #0") and press the Zone button. This just hides the density beyond some distance (e.g. 3 Angstroms) from the selected atoms.
Tom
On Feb 20, 2020, at 1:26 PM, Miriam Gochin <mgochin@lbl.gov> wrote:
Thanks for date shaming me!! It works - you guys are great. Is there any way to select certain parts of the map, if for example you just want to see the electron density of one molecule instead of all the symmetry copies?
Miriam
PS. 7 years isn't even close.
On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Miriam,
We appreciate your long use of Chimera! That bug was fixed 7 years ago. Time to install a new Chimera.
Tom
On Feb 20, 2020, at 11:46 AM, Miriam Gochin <mgochin@lbl.gov> wrote:
The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error:
NameError: global name 'step' is not defined
File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)
Hoping to figure out how to make it work.
Many thanks, --------------------------------- Miriam Gochin Touro University California / LBL miriam.gochin@tu.edu mgochin@lbl.gov 707-638-5463 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Miriam Gochin -
Tom Goddard