Axes/Planes/Centroids for the OPM membrane visualization
Dear Chimera Users,
I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM.
Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer?
Thank you for the help!
Gleb
Hi Gleb, If you define a plane it will be a plane (a flat circular disk), but it does have a slight thickness, so maybe that is what you meant by “cylindrical."
If you are trying to do something similar to this image, http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopamineReceptor.html
...you would have to define two planes, one for the outer membrane and one for the inner membrane. In the files from OPM, even though all the “membrane” points are residue DUM, different atom names are used for the inner and outer leaflets: O for the outer and N for the inner. So you can select one set of points or the other with commands like:
select :dum@o select :dum@n
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 10:27 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users,
I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM.
Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer?
Thank you for the help!
Gleb
With the latest Chimera version (1.12) I get an error message after saving a file. The error says that the file does not exist (the file didn't exist as it is being created new). The file is saved OK though.
Best
H.
-----Original Message----- From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Tuesday, October 31, 2017 4:20 PM To: James Starlight Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Axes/Planes/Centroids for the OPM membrane visualization
Hi Gleb, If you define a plane it will be a plane (a flat circular disk), but it does have a slight thickness, so maybe that is what you meant by “cylindrical."
If you are trying to do something similar to this image, http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopamineReceptor.html
...you would have to define two planes, one for the outer membrane and one for the inner membrane. In the files from OPM, even though all the “membrane” points are residue DUM, different atom names are used for the inner and outer leaflets: O for the outer and N for the inner. So you can select one set of points or the other with commands like:
select :dum@o select :dum@n
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 10:27 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users,
I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM.
Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer?
Thank you for the help!
Gleb
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Oct 31, 2017, at 2:54 PM, Hernando J Sosa hernando.sosa@einstein.yu.edu wrote:
With the latest Chimera version (1.12) I get an error message after saving a file. The error says that the file does not exist (the file didn't exist as it is being created new). The file is saved OK though.
Hi Hernando, I have managed to reproduce this. It can happen if you use an “open” dialog and then later use a “save” dialog in the same session. I will work to fix it, though as you noted it is harmless (though annoying!).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
Fixed in tomorrow’s daily build.
—Eric
On Oct 31, 2017, at 4:18 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
On Oct 31, 2017, at 2:54 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu mailto:hernando.sosa@einstein.yu.edu> wrote:
With the latest Chimera version (1.12) I get an error message after saving a file. The error says that the file does not exist (the file didn't exist as it is being created new). The file is saved OK though.
Hi Hernando, I have managed to reproduce this. It can happen if you use an “open” dialog and then later use a “save” dialog in the same session. I will work to fix it, though as you noted it is harmless (though annoying!).
—Eric
Eric Pettersen UCSF Computer Graphics Lab
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks !!
Gleb
2017-10-31 21:19 GMT+01:00 Elaine Meng meng@cgl.ucsf.edu:
Hi Gleb, If you define a plane it will be a plane (a flat circular disk), but it does have a slight thickness, so maybe that is what you meant by “cylindrical."
If you are trying to do something similar to this image, http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/dopamineReceptor/dopamineReceptor.html
...you would have to define two planes, one for the outer membrane and one for the inner membrane. In the files from OPM, even though all the “membrane” points are residue DUM, different atom names are used for the inner and outer leaflets: O for the outer and N for the inner. So you can select one set of points or the other with commands like:
select :dum@o select :dum@n
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 10:27 AM, James Starlight jmsstarlight@gmail.com wrote:
Dear Chimera Users,
I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM.
Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer?
Thank you for the help!
Gleb
participants (4)
-
Elaine Meng -
Eric Pettersen -
Hernando J Sosa -
James Starlight