Dear Chimera-X users ! I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds
5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically.
Many thanks in advance Enrico
Hi Enrico, I'd say probably the simplest way is to use the disclosure triangle for that structure in the Model Panel to show its submodels, and then close the "missing structure" submodel. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 5, 2023, at 8:52 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds
5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically.
Many thanks in advance
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello Eric, actually it's about just a single model damped from the trajectory so the problem was to eliminate unusual bond from a single pdb Enrico Il giorno mar 5 set 2023 alle ore 20:36 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, I'd say probably the simplest way is to use the disclosure triangle for that structure in the Model Panel to show its submodels, and then close the "missing structure" submodel.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 5, 2023, at 8:52 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds
5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically.
Many thanks in advance
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Eric's answer applies equally well to the case of a single PDB. Did you try what he suggested? Elaine
On Sep 6, 2023, at 12:41 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Eric,
actually it's about just a single model damped from the trajectory so the problem was to eliminate unusual bond from a single pdb
Enrico
Il giorno mar 5 set 2023 alle ore 20:36 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, I'd say probably the simplest way is to use the disclosure triangle for that structure in the Model Panel to show its submodels, and then close the "missing structure" submodel.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 5, 2023, at 8:52 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds
5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically.
Many thanks in advance
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Elaine Meng -
Enrico Martinez -
Eric Pettersen