recovering saved pseudobonds; or convert pseudo to bond?
Hi,
I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"?
Thanks, Kelly
Hi Kelly, It depends on what this cage model really is, in other words, what you mean by "manually created." If you had used the command "hkcage" or "shape icosahedron" (or the Icosahedron Surface tool), it is a mesh surface, not pseudobonds, and can be made into bonds with the command "meshmol":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html
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 Mar 25, 2011, at 5:49 AM, Kelly Dryden wrote:
Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly
Hi Elaine,
No, the model was not made in Chimera. It is a set of coordinates in a pdb file with "conect" parameters. It's actually unclear to me why some are represented as bonds and others as pseudo, but the pseudobonds are classified as "missing segments" in the PseudoBond Panel.
I would still like to be able to recover pseudobonds that have been included in a named selection when returning to a saved session.
Thanks, Kelly
On Fri, 25 Mar 2011 08:31:01 -0700 Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Kelly, It depends on what this cage model really is, in other words, what you mean by "manually created." If you had used the command "hkcage" or "shape icosahedron" (or the Icosahedron Surface tool), it is a mesh surface, not pseudobonds, and can be made into bonds with the command "meshmol":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html
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 Mar 25, 2011, at 5:49 AM, Kelly Dryden wrote:
Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly
Hi Kelly, You are right that sessions don't save the pseudobond part of selections. I will do something about that next week. In the interim I have an alternative that you'll probably like better anyway. "Missing segments" are where Chimera has judged that part of the structure is missing because the bond between two atoms is too long and there is a gap in the sequence numbering between those atoms. It shows a pseudobond in that case, but the regular bond is still there, just never displayed. Here's how to hide the pseudobonds and show the hidden actual bonds:
1) Go to Tools->General Controls->Pseudobond Panel and hide "missing segments" 2) In the command line type "sel #" to select everything in your structure 3) Type "setattr b display 2 sel" to change all bonds display mode to 2 ("smart"). The hidden bonds were in display mode 0 ("never").
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 25, 2011, at 9:10 AM, Kelly Dryden wrote:
Hi Elaine,
No, the model was not made in Chimera. It is a set of coordinates in a pdb file with "conect" parameters. It's actually unclear to me why some are represented as bonds and others as pseudo, but the pseudobonds are classified as "missing segments" in the PseudoBond Panel.
I would still like to be able to recover pseudobonds that have been included in a named selection when returning to a saved session.
Thanks, Kelly
On Fri, 25 Mar 2011 08:31:01 -0700 Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Kelly, It depends on what this cage model really is, in other words, what you mean by "manually created." If you had used the command "hkcage" or "shape icosahedron" (or the Icosahedron Surface tool), it is a mesh surface, not pseudobonds, and can be made into bonds with the command "meshmol":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html
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 Mar 25, 2011, at 5:49 AM, Kelly Dryden wrote:
Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Starting with tomorrow's 1.6 daily builds, Chimera will remember the selection status of pseudobonds.
--Eric
On Mar 25, 2011, at 10:27 AM, Eric Pettersen wrote:
Hi Kelly, You are right that sessions don't save the pseudobond part of selections. I will do something about that next week. In the interim I have an alternative that you'll probably like better anyway. "Missing segments" are where Chimera has judged that part of the structure is missing because the bond between two atoms is too long and there is a gap in the sequence numbering between those atoms. It shows a pseudobond in that case, but the regular bond is still there, just never displayed. Here's how to hide the pseudobonds and show the hidden actual bonds:
- Go to Tools->General Controls->Pseudobond Panel and hide "missing
segments" 2) In the command line type "sel #" to select everything in your structure 3) Type "setattr b display 2 sel" to change all bonds display mode to 2 ("smart"). The hidden bonds were in display mode 0 ("never").
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 25, 2011, at 9:10 AM, Kelly Dryden wrote:
Hi Elaine,
No, the model was not made in Chimera. It is a set of coordinates in a pdb file with "conect" parameters. It's actually unclear to me why some are represented as bonds and others as pseudo, but the pseudobonds are classified as "missing segments" in the PseudoBond Panel.
I would still like to be able to recover pseudobonds that have been included in a named selection when returning to a saved session.
Thanks, Kelly
On Fri, 25 Mar 2011 08:31:01 -0700 Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Kelly, It depends on what this cage model really is, in other words, what you mean by "manually created." If you had used the command "hkcage" or "shape icosahedron" (or the Icosahedron Surface tool), it is a mesh surface, not pseudobonds, and can be made into bonds with the command "meshmol":
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html
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 Mar 25, 2011, at 5:49 AM, Kelly Dryden wrote:
Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Kelly Dryden