Hi Chimera, I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command: meshmol #4 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
Hi Elaine, I am doing it no GUI via command line so I cannot select with mouse. Thanks, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command: meshmol #4 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting. I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut any of my volume because of the bounding box. I also want the biggest bounding box of two volumes. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Ryan Harlich Sent: Thursday, July 11, 2019 1:29:22 PM To: chimera-users@cgl.ucsf.edu BB Subject: RE: [Chimera-users] Finding dimensions of density map Hi Elaine, I am doing it no GUI via command line so I cannot select with mouse. Thanks, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command: meshmol #4 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
Hi Ryan, I think I did understood you: My suggestion to save the volume outline box as a molecule would give you 8 atoms at the corners, in PDB format. However, there is no similar thing to get a collective bounding box for multiple datasets. You’d just have to get a box for each volume data set and then figure out for yourself the min and max in each dimension among all the boxes. As Tom G said, if this is something you want to do repeatedly, python scripting may be the only reasonable approach. Elaine
On Jul 11, 2019, at 4:05 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting.
I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut any of my volume because of the bounding box. I also want the biggest bounding box of two volumes.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Thursday, July 11, 2019 1:29:22 PM To: chimera-users@cgl.ucsf.edu BB Subject: RE: [Chimera-users] Finding dimensions of density map
Hi Elaine,
I am doing it no GUI via command line so I cannot select with mouse.
Thanks, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, One if fine. But is there a way to do it without the GUI? The method you suggest required me to hand select the corners. I am writing a Python program so I am using --nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, July 12, 2019 9:22:38 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, I think I did understood you: My suggestion to save the volume outline box as a molecule would give you 8 atoms at the corners, in PDB format. However, there is no similar thing to get a collective bounding box for multiple datasets. You’d just have to get a box for each volume data set and then figure out for yourself the min and max in each dimension among all the boxes. As Tom G said, if this is something you want to do repeatedly, python scripting may be the only reasonable approach. Elaine
On Jul 11, 2019, at 4:05 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting.
I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut any of my volume because of the bounding box. I also want the biggest bounding box of two volumes.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Thursday, July 11, 2019 1:29:22 PM To: chimera-users@cgl.ucsf.edu BB Subject: RE: [Chimera-users] Finding dimensions of density map
Hi Elaine,
I am doing it no GUI via command line so I cannot select with mouse.
Thanks, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=qLa0zvb7%2F9qeEOWFk%2BZfEJHi%2FBAhyCPi07BJf0LuRRA%3D&reserved=0> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=fxqKjEiOqwrZJAlgyvOXl8iJrLQ0Juc8o2ZiVLVgP98%3D&reserved=0>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641027366&sdata=Dwj7EcCV%2BVVjKarHzFVO3aFLFDWhSaRmz%2FL431cIiNs%3D&reserved=0
If I’d known of another way I would have told you! The other way is to use python, as we said, but any details of that are beyond my skill set. Elaine
On Jul 12, 2019, at 1:02 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
One if fine. But is there a way to do it without the GUI? The method you suggest required me to hand select the corners. I am writing a Python program so I am using --nogui.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, July 12, 2019 9:22:38 AM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, I think I did understood you: My suggestion to save the volume outline box as a molecule would give you 8 atoms at the corners, in PDB format. However, there is no similar thing to get a collective bounding box for multiple datasets. You’d just have to get a box for each volume data set and then figure out for yourself the min and max in each dimension among all the boxes. As Tom G said, if this is something you want to do repeatedly, python scripting may be the only reasonable approach. Elaine
On Jul 11, 2019, at 4:05 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting.
I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut any of my volume because of the bounding box. I also want the biggest bounding box of two volumes.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Ryan Harlich Sent: Thursday, July 11, 2019 1:29:22 PM To: chimera-users@cgl.ucsf.edu BB Subject: RE: [Chimera-users] Finding dimensions of density map
Hi Elaine,
I am doing it no GUI via command line so I cannot select with mouse.
Thanks, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=qLa0zvb7%2F9qeEOWFk%2BZfEJHi%2FBAhyCPi07BJf0LuRRA%3D&reserved=0> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=fxqKjEiOqwrZJAlgyvOXl8iJrLQ0Juc8o2ZiVLVgP98%3D&reserved=0>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641027366&sdata=Dwj7EcCV%2BVVjKarHzFVO3aFLFDWhSaRmz%2FL431cIiNs%3D&reserved=0
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera does not have any command to make bounding boxes from fake atoms. If you want to do something this far beyond the scope of normal Chimera uses then you will have to program in Python. There is a little documentation on how to write Python programs that use Chimera capabilities that you can find by searching online. If you are new to this it will probably take you several weeks of effort to learn how to draw a simple box -- so I don't recommend pursuing that unless you are very interested. Tom
On Jul 11, 2019, at 1:29 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
I am doing it no GUI via command line so I cannot select with mouse.
Thanks, Ryan Harlich
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>>
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com <mailto:ryanharlich@hotmail.com>> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ 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>
Hi Elaine, I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command: meshmol #4 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
Hi Ryan, You did not say what you did. If using the save PDB dialog, you have to choose the model in the dialog as well as the selected-only option if you’ve used the mouse to select only the box part of the model in the window. Click Help on dialogs when you are using them and you get an error, before asking on the list. Best, Elaine
On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The help button is greyed out. Meshmol is an mrc and you said I could save it as a pdb. I don’t think this is possible. I did what you said. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, July 16, 2019 12:40:07 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Finding dimensions of density map Hi Ryan, You did not say what you did. If using the save PDB dialog, you have to choose the model in the dialog as well as the selected-only option if you’ve used the mouse to select only the box part of the model in the window. Click Help on dialogs when you are using them and you get an error, before asking on the list. Best, Elaine
On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=mBl1i29nupLseHehVLHIZXq6s9bOIbolpz7vN3O06Pg%3D&reserved=0> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=KjazTdLtJitxTNVADDbu2guA6DoBP%2BuZG7Wxgrc7G%2B4%3D&reserved=0>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=HrEFhjL4KeQX%2F%2BmguoVzB1Es%2B1ad%2BleLqv2YWHE9dZk%3D&reserved=0
Hi Ryan, The meshmol command creates a new atomic model from the mesh surface of the volume (map) model. That is the whole purpose of the meshmol command. You save the new atomic model (or its selected part) as a PDB file. Elaine
On Jul 16, 2019, at 1:39 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
The help button is greyed out. Meshmol is an mrc and you said I could save it as a pdb. I don’t think this is possible. I did what you said.
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, July 16, 2019 12:40:07 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, You did not say what you did. If using the save PDB dialog, you have to choose the model in the dialog as well as the selected-only option if you’ve used the mouse to select only the box part of the model in the window.
Click Help on dialogs when you are using them and you get an error, before asking on the list. Best, Elaine
On Jul 16, 2019, at 11:55 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Elaine,
I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.
Best, Ryan Harlich
Sent from Mail for Windows 10
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 11, 2019 12:49:19 PM To: Ryan Harlich Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Finding dimensions of density map
Hi Ryan, The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.
<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=mBl1i29nupLseHehVLHIZXq6s9bOIbolpz7vN3O06Pg%3D&reserved=0> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=KjazTdLtJitxTNVADDbu2guA6DoBP%2BuZG7Wxgrc7G%2B4%3D&reserved=0>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only as a PDB file. E.g. if the volume model is #4, command:
meshmol #4 1
then, … Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box ...use “write” command or File… Save PDB with their respective option to save only the selected part
I hope this helps, Chimera ;-) ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:
Hi Chimera,
I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?
Best, Ryan Harlich
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7C%7C942088a546f1469916f408d70a25690e%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636989028123002384&sdata=HrEFhjL4KeQX%2F%2BmguoVzB1Es%2B1ad%2BleLqv2YWHE9dZk%3D&reserved=0
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participants (3)
-
Elaine Meng -
Ryan Harlich -
Tom Goddard