Reasign secondary structure for back-bone trace
Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico
Hi Enrico, Do you have all the backbone atoms, including the backbone oxygen? What version of ChimeraX are you using? --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 17, 2023, at 7:26 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hey Eric, actually I am using a backbone subset defined by Gromacs during the computing. Are you talking about backbone or main-chain sub-space? I am using the latest version of ChimeraX but also I do have a ChimeraX daily installed on the same machine.. Cheers, Enrico Il giorno mar 17 gen 2023 alle ore 19:19 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Do you have all the backbone atoms, including the backbone oxygen? What version of ChimeraX are you using?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 17, 2023, at 7:26 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I'm talking about the oxygen connected to the non-α–carbon backbone carbon of every amino acid. If it is missing, dssp will not compute secondary structure. --Eric
On Jan 18, 2023, at 1:10 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hey Eric, actually I am using a backbone subset defined by Gromacs during the computing. Are you talking about backbone or main-chain sub-space? I am using the latest version of ChimeraX but also I do have a ChimeraX daily installed on the same machine.. Cheers, Enrico
Il giorno mar 17 gen 2023 alle ore 19:19 Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> ha scritto: Hi Enrico, Do you have all the backbone atoms, including the backbone oxygen? What version of ChimeraX are you using?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 17, 2023, at 7:26 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
I gotcha, indeed It corresponds to the main-chain atom subset. With it everything is OK! Cheers Enrico Il giorno gio 19 gen 2023 alle ore 01:11 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
I'm talking about the oxygen connected to the non-α–carbon backbone carbon of every amino acid. If it is missing, dssp will not compute secondary structure.
--Eric
On Jan 18, 2023, at 1:10 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hey Eric, actually I am using a backbone subset defined by Gromacs during the computing. Are you talking about backbone or main-chain sub-space? I am using the latest version of ChimeraX but also I do have a ChimeraX daily installed on the same machine.. Cheers, Enrico
Il giorno mar 17 gen 2023 alle ore 19:19 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Do you have all the backbone atoms, including the backbone oxygen? What version of ChimeraX are you using?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 17, 2023, at 7:26 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users! I am working on the visualization of a trajectory containing only back-bone atoms of the protein obtained from the PCA. When I load this multi-pdb ensemble to Chimera-X I can see only back-bone traces without any secondary structure information. I've tried to use dssp command to re-assign the secondary structure but it did not change the visualization state. Would it be possible to do it in some automatic fashion via some built-in command? Many thanks in advance Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Enrico Martinez -
Eric Pettersen