Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan
Hi Megan, The "vop cover" command (actually "volume cover" in ChimeraX, but both will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:
volume cover #1 atomBox #2
You can see the help for "volume cover" by using the command "help volume cover" ... or the same thing on our website here: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover
That manual page shows the command syntax and explains the options. The "volume-spec" in the usage is the map model number.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2020, at 7:42 AM, Megan Mayer mmayer@nanoimagingservices.com wrote:
Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan
Dear Elaine, Thank you very much! I was able to use this vop command for my movie effectively.
Another question if you have a moment: After showing the field of view of my entire model, I am trying to zoom/pan/focus into a specific point on my model (a sulphur atom, which has a marker #3). I see in the chimera instructions for "view" ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#initial) that I should be able to focus onto a specific point, but I am not sure how to specify the sulphur atom marker. Also, is there a way to define the field of view?
"view spec" --> "view #3 models" returns me an error "expected an integer
= 1 or a keyword
Any help or point in the right direction greatly appreciated !!
Best, Megan
On Tue, Jul 28, 2020 at 11:07 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Megan, The "vop cover" command (actually "volume cover" in ChimeraX, but both will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:
volume cover #1 atomBox #2
You can see the help for "volume cover" by using the command "help volume cover" ... or the same thing on our website here: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover
That manual page shows the command syntax and explains the options. The "volume-spec" in the usage is the map model number.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2020, at 7:42 AM, Megan Mayer mmayer@nanoimagingservices.com
wrote:
Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with atomic
structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to
expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan
Hi Megan, If the marker is model #3 (the whole model is just that marker) then "spec" is just #3. The "view" command does not take a "models" keyword, and the "#" symbol itself means model number. http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
view #3
If model #3 has other markers or atoms in it, maybe you want to also specify the residue number of your specific marker, which you can probably see by hovering the mouse over it to see a balloon with its information. E.g. if its residue number is 4,
view #3:4
However, focusing the view on just a single atom or marker will give you an extreme close-up, including narrowing the space between front and back clip planes. You can turn off the clipping with command "clip off" (without any other words). To focus on your marker but not with such an extreme closeup, maybe you instead want something like this (assuming the marker = model #3):
view #3 clip false; zoom .3 - or - view #3 :< 2.5 clip false
clip false is explained in the view manual page, the zoom command zooms back out, and "#3 :< 2.5" means residues within 2.5 angstroms of #3, see specification by zone. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 29, 2020, at 7:23 AM, Megan Mayer mmayer@nanoimagingservices.com wrote:
Dear Elaine, Thank you very much! I was able to use this vop command for my movie effectively.
Another question if you have a moment: After showing the field of view of my entire model, I am trying to zoom/pan/focus into a specific point on my model (a sulphur atom, which has a marker #3). I see in the chimera instructions for "view" (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#initial) that I should be able to focus onto a specific point, but I am not sure how to specify the sulphur atom marker. Also, is there a way to define the field of view?
"view spec" --> "view #3 models" returns me an error "expected an integer >= 1 or a keyword
Any help or point in the right direction greatly appreciated !!
Best, Megan
On Tue, Jul 28, 2020 at 11:07 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Megan, The "vop cover" command (actually "volume cover" in ChimeraX, but both will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:
volume cover #1 atomBox #2
You can see the help for "volume cover" by using the command "help volume cover" ... or the same thing on our website here: http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover
That manual page shows the command syntax and explains the options. The "volume-spec" in the usage is the map model number.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2020, at 7:42 AM, Megan Mayer mmayer@nanoimagingservices.com wrote:
Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan
Hi Elaine, again, thank you very much. The hover tool is incredibly useful. I am now able to zoom the the sulphur atom.
However, is there a way to slowly zoom from the entire structure, to the desired model number, in my video? Here is the example of what I use, but isn't quite right (i attached an example movie):
#zoom into specific area then zoom back out to original
movie record ; view orient ; wait 20 ; zoom 1.2 100; view #3 clip false ; wait 20; view orient ; movie encode ~/
Thank you very much, Megan
Megan Mayer, M.S. Microscopist, Cryo-EM NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 888-675-8261
On Wed, Jul 29, 2020 at 12:37 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Megan, If the marker is model #3 (the whole model is just that marker) then "spec" is just #3. The "view" command does not take a "models" keyword, and the "#" symbol itself means model number. http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
view #3
If model #3 has other markers or atoms in it, maybe you want to also specify the residue number of your specific marker, which you can probably see by hovering the mouse over it to see a balloon with its information. E.g. if its residue number is 4,
view #3:4
However, focusing the view on just a single atom or marker will give you an extreme close-up, including narrowing the space between front and back clip planes. You can turn off the clipping with command "clip off" (without any other words). To focus on your marker but not with such an extreme closeup, maybe you instead want something like this (assuming the marker = model #3):
view #3 clip false; zoom .3
- or -
view #3 :< 2.5 clip false
clip false is explained in the view manual page, the zoom command zooms back out, and "#3 :< 2.5" means residues within 2.5 angstroms of #3, see specification by zone. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 29, 2020, at 7:23 AM, Megan Mayer mmayer@nanoimagingservices.com
wrote:
Dear Elaine, Thank you very much! I was able to use this vop command for
my movie effectively.
Another question if you have a moment: After showing the field of view
of my entire model, I am trying to zoom/pan/focus into a specific point on my model (a sulphur atom, which has a marker #3). I see in the chimera instructions for "view" ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#initial) that I should be able to focus onto a specific point, but I am not sure how to specify the sulphur atom marker. Also, is there a way to define the field of view?
"view spec" --> "view #3 models" returns me an error "expected an
integer >= 1 or a keyword
Any help or point in the right direction greatly appreciated !!
Best, Megan
On Tue, Jul 28, 2020 at 11:07 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Megan, The "vop cover" command (actually "volume cover" in ChimeraX, but both
will work) needs both the map model number and the atomic model number. So if your map model is #1 and the atomic model is #2, maybe something like:
volume cover #1 atomBox #2
You can see the help for "volume cover" by using the command "help
volume cover" ... or the same thing on our website here:
http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover
That manual page shows the command syntax and explains the options. The
"volume-spec" in the usage is the map model number.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2020, at 7:42 AM, Megan Mayer <
mmayer@nanoimagingservices.com> wrote:
Hi chimeraX forum,
I am trying to get an electron density map (.mrc) to overlap with
atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule.
I am thinking to use the "vop cover" command to get the density to
expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response.
Thanks in advance for any help!!
Megan
You can save multiple views with different names (see "view name") and then gradually transition between them using "view" and "frames" with some number of frames.
This is all explained in the "view" manual page http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
See also "making movies" and links therein to movie tutorials: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Several commands have frame arguments directly within them, or if they don't, you can combine them with "perframe" commands for a repeated action.
Making movie scripts is generally an iterative process with many adjustments and replays. One wouldn't expect to just look at a script and predict the exact command to make it look how somebody else wants it to look.
I hope this helps, Elaine
On Jul 29, 2020, at 11:19 AM, Megan Mayer mmayer@nanoimagingservices.com wrote:
Hi Elaine, again, thank you very much. The hover tool is incredibly useful. I am now able to zoom the the sulphur atom.
However, is there a way to slowly zoom from the entire structure, to the desired model number, in my video? Here is the example of what I use, but isn't quite right (i attached an example movie):
#zoom into specific area then zoom back out to original
movie record ; view orient ; wait 20 ; zoom 1.2 100; view #3 clip false ; wait 20; view orient ; movie encode ~/ Thank you very much, Megan
Hi Elaine... the "view name 'NAME' " and "view 'NAME'" pair of commands turned out to be exactly what I needed. Sorry I did not fully understand the manual at first glance...
Thanks!!
Megan
On Wed, Jul 29, 2020 at 2:55 PM Elaine Meng meng@cgl.ucsf.edu wrote:
You can save multiple views with different names (see "view name") and then gradually transition between them using "view" and "frames" with some number of frames.
This is all explained in the "view" manual page http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
See also "making movies" and links therein to movie tutorials: http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
Several commands have frame arguments directly within them, or if they don't, you can combine them with "perframe" commands for a repeated action.
Making movie scripts is generally an iterative process with many adjustments and replays. One wouldn't expect to just look at a script and predict the exact command to make it look how somebody else wants it to look.
I hope this helps, Elaine
On Jul 29, 2020, at 11:19 AM, Megan Mayer <
mmayer@nanoimagingservices.com> wrote:
Hi Elaine, again, thank you very much. The hover tool is incredibly
useful. I am now able to zoom the the sulphur atom.
However, is there a way to slowly zoom from the entire structure, to the
desired model number, in my video? Here is the example of what I use, but isn't quite right (i attached an example movie):
#zoom into specific area then zoom back out to original
movie record ; view orient ; wait 20 ; zoom 1.2 100; view #3 clip false
; wait 20; view orient ; movie encode ~/
Thank you very much, Megan
participants (2)
-
Elaine Meng
-
Megan Mayer