Re: [chimerax-users] [Chimera-users] Creating Bonds between Models
Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#join
The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning.
By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users@cgl.ucsf.edu CC'd here.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello, I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! Best regards, Draven Houser
Hello Elaine,
Thank you for your reply. I can probably do this in the old Chimera (and I'll refer to the other mailing list for ChimeraX for those questions in the future). However, it doesn't seem as if the combine command for ChimeraX is available on the mac version yet unless I am misunderstanding the syntax (taken from https://www.cgl.ucsf.edu/chimerax/docs/user/commands/combine.html). When I type "help combine" or "combine" or such, even when followed by the model IDs and names as listed, it says command not recognized. Is this only available for windows at the moment? Again, thank you for all your help.
Best regards, Draven
On Mon, Apr 25, 2022 at 4:08 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: < https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#j...
The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning.
By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users@cgl.ucsf.edu CC'd here.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hello, I am trying to build a structure in chimeraX that is a combination of
several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks!
Best regards, Draven Houser
CAUTION: EXTERNAL SENDER Do not click any links, open any attachments, or REPLY to the message unless you trust the sender and know the content is safe.
Hi Draven, The documentation is for the current development version of ChimeraX. You probably have a very old version, since according to the Change Log, the combine command was added in July 2021:
https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Thus you need to get version 1.3 or the daily build for the "combine" command, but only the daily build (1.4 in progress) would have the "build join peptide" command. I haven't put the latter in the change log yet since it's still being tested.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2022, at 2:23 PM, Draven Houser via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello Elaine,
Thank you for your reply. I can probably do this in the old Chimera (and I'll refer to the other mailing list for ChimeraX for those questions in the future). However, it doesn't seem as if the combine command for ChimeraX is available on the mac version yet unless I am misunderstanding the syntax (taken from https://www.cgl.ucsf.edu/chimerax/docs/user/commands/combine.html). When I type "help combine" or "combine" or such, even when followed by the model IDs and names as listed, it says command not recognized. Is this only available for windows at the moment? Again, thank you for all your help.
Best regards, Draven
On Mon, Apr 25, 2022 at 4:08 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#join
The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning.
By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users@cgl.ucsf.edu CC'd here.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello, I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! Best regards, Draven Houser
CAUTION: EXTERNAL SENDER Do not click any links, open any attachments, or REPLY to the message unless you trust the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
The problem with specifying "phi" in the "build join peptide" command has been fixed, and this fix will be in the next daily build of ChimeraX.
Elaine
On Apr 25, 2022, at 1:08 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#join
The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning.
By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users@cgl.ucsf.edu CC'd here.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hello, I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! Best regards, Draven Houser
participants (2)
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Draven Houser -
Elaine Meng