Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich
Hi Rich, That is the whole purpose of the tool, to view axes and other derived objects and perform measurements between them. The axis or axes should be displayed as cylinders and listed in the Structure Measurements dialog as soon as you define them. Perhaps you are doing something wrong? Here is the documentation for Axes/Planes in Chimera 1.4: <http://www.cgl.ucsf.edu/chimera/1.4/docs/ContributedSoftware/structuremeas/s...
and in Chimera 1.5 (daily builds), it has been expanded to Axes/Planes/ Centroids: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
The dialog listing the axes includes color wells for changing their colors and allows choosing two axes and getting distances/angles. If you get Chimera version 1.5, you can also make the measurements involving axes with the "distance" and "angle" commands. 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 Feb 23, 2010, at 9:51 AM, Richard Stanton wrote:
Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich
Thanks Elaine, but I still cannot get the axis to display. Would it matter that I have defined it using multiple models? I have attached a screen shot with the structure measurement window open and my "axis_GDP" plane defined and the "shown" box checked but there is no cylinder. I have made a polymeric structure of many separate protein models and am tying to link them using vectors. Thanks, Rich ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, February 23, 2010 1:18 PM To: Richard Stanton Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Rendering a vector/axis Hi Rich, That is the whole purpose of the tool, to view axes and other derived objects and perform measurements between them. The axis or axes should be displayed as cylinders and listed in the Structure Measurements dialog as soon as you define them. Perhaps you are doing something wrong? Here is the documentation for Axes/Planes in Chimera 1.4: <http://www.cgl.ucsf.edu/chimera/1.4/docs/ContributedSoftware/structuremeas/s...
and in Chimera 1.5 (daily builds), it has been expanded to Axes/Planes/ Centroids: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
The dialog listing the axes includes color wells for changing their colors and allows choosing two axes and getting distances/angles. If you get Chimera version 1.5, you can also make the measurements involving axes with the "distance" and "angle" commands. 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 Feb 23, 2010, at 9:51 AM, Richard Stanton wrote:
Hi, Is there a way to render a vector after defining it as an axis in the "Axes/Planes" tab under "Structure Measurements"? I am able to define an axis using the selected atoms in my structure but I am not sure how to visually render and alter its appearance, as there is no visual representation on the graphics screen. I was hoping that after using my selected atoms to define the axis I would then have an arrow or line showing me the axis/vector and I could then create different vectors/axis and view them simultaneously to show the difference between their angles. Is there a way to do this? Thanks in advance for the help! Thanks, Rich
On Feb 23, 2010, at 10:36 AM, Richard Stanton wrote:
Thanks Elaine, but I still cannot get the axis to display. Would it matter that I have defined it using multiple models?
Indeed it would since it seems that defining axes involving multiple models is buggy. It is creating an axis but is mispositioning/ miscalculating it. In your case it is so badly positioned that you can't see it in the view you have. I will be fixing this either today or in the next day or two. Regardless I will be opening a ticket in our bug database with you on the cc list so you will know when it gets fixed. In the interim you can work around the problem by combining the models into one (either with the "copy/combine" button of the Model Panel or with the "combine" command). The axis will be correctly computed/ shown when you use the combined model. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
-
Elaine Meng -
Eric Pettersen -
Richard Stanton