How to define axes in chimeraX
Hi,
I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools • Structure analysis • Axes/Planes/Centroids • Define axes
But I wasn’t able to find out the equivalent function in chimeraX. Would you please direct me to that function in ChimeraX?
Thank you so much! Best regards, Bingchun
Bingchun Zhao, PhD Postdoctoral, VF Biodefense Research Section VRC/NIAID/NIH Bldg 40, Room 2607B 40 Convent Drive Bethesda, MD 20892 Tel: 301-761-7649 Email: bingchun.zhao@nih.govmailto:bingchun.zhao@nih.gov
Hi Bingchun, ChimeraX is newer and under development, and doesn't (yet) contain some of the features of Chimera. Some of these are listed in the "Missing Features" section of the ChimeraX download page: https://www.rbvi.ucsf.edu/chimerax/download.html
ChimeraX does not yet have any graphical tool interface to calculating axes, but it does have the "define axes" command and the ability to measure angles and distances of the resulting axes with the "distance" and "angle" commands. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html
The "define axis" command was added after the 1.3 release, so you have to download the newer 1.4 daily build to use it. https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Example commands: open 2gbp define axis #1 perHelix true
....then in the Model Panel you can see the axes are under model #1.2, e.g. "helix 1" is #1.2.1, "helix 2" is #1.2.2, etc. Example command to measure an axis-axis angle:
angle #1.2.1 #1.2.5
You can use any set of atoms to calculate an axis -- i.e. it does not have to be a helix. See the "define axis" help above for different options of the 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 Feb 10, 2022, at 1:00 PM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools Structure analysis Axes/Planes/Centroids Define axes
But I wasn’t able to find out the equivalent function in chimeraX. Would you please direct me to that function in ChimeraX?
Thank you so much! Best regards, Bingchun
Thank you so much for the direciton, Elaine! This is very helpful! Best regards, Bingchun
On 2/10/22, 5:36 PM, "Elaine Meng" meng@cgl.ucsf.edu wrote:
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Hi Bingchun, ChimeraX is newer and under development, and doesn't (yet) contain some of the features of Chimera. Some of these are listed in the "Missing Features" section of the ChimeraX download page: https://www.rbvi.ucsf.edu/chimerax/download.html
ChimeraX does not yet have any graphical tool interface to calculating axes, but it does have the "define axes" command and the ability to measure angles and distances of the resulting axes with the "distance" and "angle" commands. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#axis https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html
The "define axis" command was added after the 1.3 release, so you have to download the newer 1.4 daily build to use it. https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Example commands: open 2gbp define axis #1 perHelix true
....then in the Model Panel you can see the axes are under model #1.2, e.g. "helix 1" is #1.2.1, "helix 2" is #1.2.2, etc. Example command to measure an axis-axis angle:
angle #1.2.1 #1.2.5
You can use any set of atoms to calculate an axis -- i.e. it does not have to be a helix. See the "define axis" help above for different options of the 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 Feb 10, 2022, at 1:00 PM, Zhao, Bingchun (NIH/VRC) [F] via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: > > Hi, > > I’ve been using Chimera to define the axes of my model, then to calculate the angle of approach, by using Tools Structure analysis Axes/Planes/Centroids Define axes > > But I wasn’t able to find out the equivalent function in chimeraX. > Would you please direct me to that function in ChimeraX? > > Thank you so much! > Best regards, > Bingchun >
participants (2)
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Elaine Meng -
Zhao, Bingchun (NIH/VRC) [F]