Re: [Chimera-users] Display a spider volume data in a specific orientation
Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform...
It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation.
I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0
You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used.
I'm CC-ing the chimera-users@cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:
Hi Elaine, I have a spider volume data (or mrc density map) from which I got a serious 2D projections. I have the Euler angles for each projection. Is there a way in Chimera that I can use those Euler angles to display the 3D spider volume data (or mrc density map) in a specific orientation that corresponding to that 2D projection? Thank you very much in advance. Best, Zongli
Zongli Li, Ph.D.
Howard Hughes Medical Institute Department of Cell Biology Harvard Medical School C Building, Room 420B 240 Longwood Avenue Boston, MA 02115
Tel: 617-432-4095 (Office) 617-432-4708 (EM Suite) 617-432-4091 (Computer room) Fax: 617-432-1144 Email: zongli_li@hms.harvard.edu
Thanks a lot, Elaine. I'll try it your way before I got other suggestions.
Best,
Zongli
________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Wednesday, April 07, 2010 3:30 PM To: Li, Zongli Cc: Chimera BB Subject: Re: Display a spider volume data in a specific orientation
Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform...
It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation.
I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0
You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used.
I'm CC-ing the chimera-users@cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:
Hi Elaine, I have a spider volume data (or mrc density map) from which I got a serious 2D projections. I have the Euler angles for each projection. Is there a way in Chimera that I can use those Euler angles to display the 3D spider volume data (or mrc density map) in a specific orientation that corresponding to that 2D projection? Thank you very much in advance. Best, Zongli
Zongli Li, Ph.D.
Howard Hughes Medical Institute Department of Cell Biology Harvard Medical School C Building, Room 420B 240 Longwood Avenue Boston, MA 02115
Tel: 617-432-4095 (Office) 617-432-4708 (EM Suite) 617-432-4091 (Computer room) Fax: 617-432-1144 Email: zongli_li@hms.harvard.edu
Hi Zongli,
I've improved the Chimera Transform Molecule Coordinates dialog to allow using Euler angles to reorient volume data and other non-molecule models. The dialog has been renamed to "Transform Coordinates" and is under the Tools / Movement menu. You can get this improved version in tomorrow's Chimera daily build.
There are alternate Euler angle conventions. Chimera only uses the chi-convention as described in the Chimera manual:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/transform/t...
"Euler angles [? ? ?] - rotations defined by the ?-convention, where the first rotation is by an angle ? about the Z-axis, the second is by an angle ? (potentially ranging from 0 to ?) about the new X-axis, and the third is by an angle ? about the new Z-axis."
Hope this is the Euler angle convention you are using.
Tom
Thanks a lot, Elaine. I'll try it your way before I got other suggestions.
Best,
Zongli
From: Elaine Meng Sent: Wednesday, April 07, 2010 3:30 PM To: Li, Zongli Cc: Chimera BB Subject: Re: Display a spider volume data in a specific orientation
Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transform...
It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation.
I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0
You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used.
I'm CC-ing the chimera-users@cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer!
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2010, at 11:51 AM, Li, Zongli wrote:
Hi Elaine, I have a spider volume data (or mrc density map) from which I got a serious 2D projections. I have the Euler angles for each projection. Is there a way in Chimera that I can use those Euler angles to display the 3D spider volume data (or mrc density map) in a specific orientation that corresponding to that 2D projection? Thank you very much in advance. Best, Zongli
Zongli Li, Ph.D.
Howard Hughes Medical Institute Department of Cell Biology Harvard Medical School C Building, Room 420B 240 Longwood Avenue Boston, MA 02115
Hi Elaine,
I try to set values below certain level to 0 in a EM density map (mrc format) using vop threshold:
vop threshold #0 min 0.00007 set 0
But I got an error message:
Unknown vop operation: threshold
The Chimera version: candidate version 1.7 (build 38162) 2013-01-25 00:38:47 UTC
Could you please help me out?
Thank you very much!
Zongli
Hi Zongli, It is saying that the command option is not available in the version of Chimera that you are using, apparently a 1.7 candidate. From looking at the release notes (Command Changes section), I see that "vop threshold" was added in Chimera 1.8. So you need to get Chimera 1.8 or newer!
http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.8.html http://www.rbvi.ucsf.edu/chimera/download.html
If you want the documentation to match what you have downloaded, use the Chimera Help menu. If you are looking at documentation online, it might not match what you have. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 8, 2014, at 9:26 AM, "Li, Zongli" Zongli_Li@hms.harvard.edu wrote:
Hi Elaine, I try to set values below certain level to 0 in a EM density map (mrc format) using vop threshold:
vop threshold #0 min 0.00007 set 0
But I got an error message:
Unknown vop operation: threshold
The Chimera version: candidate version 1.7 (build 38162) 2013-01-25 00:38:47 UTC
Could you please help me out? Thank you very much! Zongli
Hi Elaine,
Thanks a lot!
Best regards,
Zongli ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, May 08, 2014 12:37 PM To: Li, Zongli Cc: Chimera BB Subject: Re: vop threshold
Hi Zongli, It is saying that the command option is not available in the version of Chimera that you are using, apparently a 1.7 candidate. From looking at the release notes (Command Changes section), I see that "vop threshold" was added in Chimera 1.8. So you need to get Chimera 1.8 or newer!
http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.8.html http://www.rbvi.ucsf.edu/chimera/download.html
If you want the documentation to match what you have downloaded, use the Chimera Help menu. If you are looking at documentation online, it might not match what you have. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 8, 2014, at 9:26 AM, "Li, Zongli" Zongli_Li@hms.harvard.edu wrote:
Hi Elaine, I try to set values below certain level to 0 in a EM density map (mrc format) using vop threshold:
vop threshold #0 min 0.00007 set 0
But I got an error message:
Unknown vop operation: threshold
The Chimera version: candidate version 1.7 (build 38162) 2013-01-25 00:38:47 UTC
Could you please help me out? Thank you very much! Zongli
participants (3)
-
Elaine Meng -
Li, Zongli -
Tom Goddard