Dear ChimeraX group,
My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: [cid:image001.png@01D8CD9D.17E4A690]
I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
Best, Tianming
Hi Tianming, You didn't say what your coloring means: whether it is color by distance or some property. However, you can get parts of a map by various different methods:
(1) volume zone (hide some parts by some distance from some atoms) https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone
(2) interactively using the Map Eraser tool to set some parts to zero https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#erase
(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume" https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html
I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX group,
My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: <image001.png>
I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
Best, Tianming
Hi Dr. Elaine,
I tried the way you suggested, it is helpful. One more question is that, the one I am trying to work on now, the colored map, is a density map read from .dx file. Is there any way I can save the edited map (aftering cropping and erasing) as a new .dx file?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 上午11:12 收件人: Tianming Qu tqu@fsu.edu 抄送: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu 主题: cropping map to red part Hi Tianming, You didn't say what your coloring means: whether it is color by distance or some property. However, you can get parts of a map by various different methods:
(1) volume zone (hide some parts by some distance from some atoms) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively using the Map Eraser tool to set some parts to zero <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume" <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/v... >
I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX group,
My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: <image001.png>
I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
Best, Tianming
Hi Tianming, Sorry no, ChimeraX can save maps (volume data) in several formats, but not .dx
You can use command "save formats" to list the possible formats in the Log, or see the list at our website here: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mapformats
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 11:52 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Elaine,
I tried the way you suggested, it is helpful. One more question is that, the one I am trying to work on now, the colored map, is a density map read from .dx file. Is there any way I can save the edited map (aftering cropping and erasing) as a new .dx file?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 上午11:12 收件人: Tianming Qu tqu@fsu.edu 抄送: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu 主题: cropping map to red part
Hi Tianming, You didn't say what your coloring means: whether it is color by distance or some property. However, you can get parts of a map by various different methods:
(1) volume zone (hide some parts by some distance from some atoms) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively using the Map Eraser tool to set some parts to zero <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume" <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/v... >
I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings! I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX group,
My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: <image001.png>
I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
Best, Tianming
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午3:09 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: Re: [chimerax-users] cropping map to red part Hi Tianming, Sorry no, ChimeraX can save maps (volume data) in several formats, but not .dx
You can use command "save formats" to list the possible formats in the Log, or see the list at our website here: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 11:52 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Elaine,
I tried the way you suggested, it is helpful. One more question is that, the one I am trying to work on now, the colored map, is a density map read from .dx file. Is there any way I can save the edited map (aftering cropping and erasing) as a new .dx file?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 上午11:12 收件人: Tianming Qu tqu@fsu.edu 抄送: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu 主题: cropping map to red part
Hi Tianming, You didn't say what your coloring means: whether it is color by distance or some property. However, you can get parts of a map by various different methods:
(1) volume zone (hide some parts by some distance from some atoms) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively using the Map Eraser tool to set some parts to zero <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
(2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume" <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/v... >
I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings! I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX group,
My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: <image001.png>
I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.
Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.
Best, Tianming
If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. https://rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume
See also the general page on measurements: https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig. [图片包含 游戏机, 项链, 电话 描述已自动生成]
Best, Tianming 发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:10 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: calculate volume of voxels If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
Yes, that is the volume inside the surface, my second suggestion. It depends on the contour level of the surface, of course.
Elaine
On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig. <image001.png>
Best, Tianming 发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:10 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: calculate volume of voxels
If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks for the help Dr. Elaine,
Is there any way I can figure out the coordinates of each voxel?
I know from mdanalysis, if one knows the voxel size (delta) and delta of one voxel cell, the voxel center coordinates can be calculated. Can I do the same way in ChimeraX?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:18 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: Re: [chimerax-users] calculate volume of voxels Yes, that is the volume inside the surface, my second suggestion. It depends on the contour level of the surface, of course.
Elaine
On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig. <image001.png>
Best, Tianming 发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:10 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: calculate volume of voxels
If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!03B7yr-Dfa3eZffX75Ds2z7GS0qgRXfkjOjkvt6b-NRbZiKRnRPeQrRutR-B_h04w70LE7k-L-mNIA$
Hi Tianming, I do not know what you mean by "voxel."
If you want to find out the coordinates of some point on the surface, you can put a marker (a dummy atom) on that point, see Marker Placement tool and the Markers tab of the Toolbar icons across the top of the ChimeraX window: https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html
The third icon in that tab is for "mark surface", you would click that icon to assign the function to right-mouse click (= trackpad + Alt on Windows, trackpad + command key on Mac). Then you can right-mouse-click a point on the surface to place the marker.
...and then find out the marker coordinates, for example by selecting it (Ctrl-click) and then using command:
getcrd sel
If you just mean the locations of the grid points in your map, you can calculate that yourself from the information in the Map Coordinates tool mentioned in my earlier reply.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2022, at 7:56 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the help Dr. Elaine,
Is there any way I can figure out the coordinates of each voxel?
I know from mdanalysis, if one knows the voxel size (delta) and delta of one voxel cell, the voxel center coordinates can be calculated. Can I do the same way in ChimeraX?
Best, Tianming
Hi Dr.Elaine,
Thanks for the help.
One more question is that, is there any way I can convert the .mrc file to a .dx file?
Best, Tianming
发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期四, 2022年9月22日 上午11:25 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: get coordinates of voxel Hi Tianming, I do not know what you mean by "voxel."
If you want to find out the coordinates of some point on the surface, you can put a marker (a dummy atom) on that point, see Marker Placement tool and the Markers tab of the Toolbar icons across the top of the ChimeraX window: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
The third icon in that tab is for "mark surface", you would click that icon to assign the function to right-mouse click (= trackpad + Alt on Windows, trackpad + command key on Mac). Then you can right-mouse-click a point on the surface to place the marker.
...and then find out the marker coordinates, for example by selecting it (Ctrl-click) and then using command:
getcrd sel
If you just mean the locations of the grid points in your map, you can calculate that yourself from the information in the Map Coordinates tool mentioned in my earlier reply.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2022, at 7:56 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the help Dr. Elaine,
Is there any way I can figure out the coordinates of each voxel?
I know from mdanalysis, if one knows the voxel size (delta) and delta of one voxel cell, the voxel center coordinates can be calculated. Can I do the same way in ChimeraX?
Best, Tianming
Hi Tianming, Maybe some other program would do it, but ChimeraX does not convert mrc to dx, because it does not write the dx format.
As mentioned before, you can list in the Log the formats that ChimeraX can write with command "save formats" or see the list here on our website: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats
I changed the subject line because it may be useful to others if it matches the subject that is being discussed. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2022, at 6:31 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr.Elaine,
Thanks for the help.
One more question is that, is there any way I can convert the .mrc file to a .dx file?
Best, Tianming
Hello !
Vmd Can actually do that, if you install VMD then you can use the "mdff" function with "mdff griddx -i INPUTMAP.mrc -o OUTPUTMAP.dx"
Best, Thibault Tubiana.
----- Mail original ----- De: "Elaine Meng via ChimeraX-users" chimerax-users@cgl.ucsf.edu À: "Tianming Qu" tqu@fsu.edu Cc: "ChimeraX Users Help" chimerax-users@cgl.ucsf.edu Envoyé: Vendredi 23 Septembre 2022 17:36:53 Objet: [chimerax-users] convert mrc to dx?
Hi Tianming, Maybe some other program would do it, but ChimeraX does not convert mrc to dx, because it does not write the dx format.
As mentioned before, you can list in the Log the formats that ChimeraX can write with command "save formats" or see the list here on our website: https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats
I changed the subject line because it may be useful to others if it matches the subject that is being discussed. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2022, at 6:31 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr.Elaine,
Thanks for the help.
One more question is that, is there any way I can convert the .mrc file to a .dx file?
Best, Tianming
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Also, I notice that there are some python modules in chimerax, can I import them in to my own python code ?
Best, Tianming 发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:18 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: Re: [chimerax-users] calculate volume of voxels Yes, that is the volume inside the surface, my second suggestion. It depends on the contour level of the surface, of course.
Elaine
On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig. <image001.png>
Best, Tianming 发件人: Elaine Meng meng@cgl.ucsf.edu 日期: 星期三, 2022年9月21日 下午4:10 收件人: Tianming Qu tqu@fsu.edu 抄送: ChimeraX Users Help chimerax-users@cgl.ucsf.edu 主题: calculate volume of voxels
If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!03B7yr-Dfa3eZffX75Ds2z7GS0qgRXfkjOjkvt6b-NRbZiKRnRPeQrRutR-B_h04w70LE7k-L-mNIA$
Yes, ChimeraX modules are importable in user scripts and will work as long as you run the script with ChimeraX.
— Zach
On Sep 22, 2022, at 08:21, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Also, I notice that there are some python modules in chimerax, can I import them in to my own python code ?
Best, Tianming 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 日期: 星期三, 2022年9月21日 下午4:18 收件人: Tianming Qu <tqu@fsu.edu mailto:tqu@fsu.edu> 抄送: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> 主题: Re: [chimerax-users] calculate volume of voxels
Yes, that is the volume inside the surface, my second suggestion. It depends on the contour level of the surface, of course.
Elaine
On Sep 21, 2022, at 1:15 PM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Not only the voxel map, but also the whole region of the map, for example the colume of the blue region in the following fig. <image001.png>
Best, Tianming 发件人: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> 日期: 星期三, 2022年9月21日 下午4:10 收件人: Tianming Qu <tqu@fsu.edu mailto:tqu@fsu.edu> 抄送: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> 主题: calculate volume of voxels
If you mean to just find out the voxel size, you can use command "volume settings" or menu: Tools... Volume Data... Map Coordinates. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
If you mean to measure the volume inside the surface (cubic angstroms) then command "measure volume" or menu: Tools... Volume Data... Measure Volume and Area. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... >
See also the general page on measurements: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/measure... >
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2022, at 12:18 PM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
Thanks for the so quick reply Dr. Elaine.
One more question, can chimera calculate the volume of voxels for density map?
Best, Tianming
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participants (4)
-
Elaine Meng -
Thibault TUBIANA -
Tianming Qu -
Zach Pearson