morph with molecular surface for part of molecule
How can I generate a morph with a molecular surface representation? many thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege
Hi Susan, Unfortunately it’s not as friendly as Chimera (yet). You would need to force recomputing the surface at each trajectory frame, for example with commands like the following for morph trajectory model #3: alias stuff surf close; surf #3 & protein perframe stuff; coordset #3 1,21; wait 21; ~perframe In that example I first create an alias “stuff” (could be some other word) that includes all the actions I want to do at each frame, then define it as a per-frame action to occur at each step of trajectory playback with the “coordset” command. The “wait” is required so that stopping the perframe action with “~perframe” won’t happen until after all the trajectory frames are played. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/wait.html> Closing the surface is also required because otherwise “surface” thinks it doesn’t need to do anything because a surface for the same set of atoms is already there… it isn’t smart enough (yet) to realize that the atoms may have moved around. 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 29, 2019, at 8:52 AM, Susan Lea <susan.lea@path.ox.ac.uk> wrote:
How can I generate a morph with a molecular surface representation?
many thanks Susan
Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, this is great - nearly what I want! Now I'm getting fussy and want to color a residue on the surface but can't seem to get the colouring to stick.... any ideas? thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 29 April 2019 23:27:49 To: Susan Lea Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] morph with molecular surface for part of molecule Hi Susan, Unfortunately it’s not as friendly as Chimera (yet). You would need to force recomputing the surface at each trajectory frame, for example with commands like the following for morph trajectory model #3: alias stuff surf close; surf #3 & protein perframe stuff; coordset #3 1,21; wait 21; ~perframe In that example I first create an alias “stuff” (could be some other word) that includes all the actions I want to do at each frame, then define it as a per-frame action to occur at each step of trajectory playback with the “coordset” command. The “wait” is required so that stopping the perframe action with “~perframe” won’t happen until after all the trajectory frames are played. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/wait.html> Closing the surface is also required because otherwise “surface” thinks it doesn’t need to do anything because a surface for the same set of atoms is already there… it isn’t smart enough (yet) to realize that the atoms may have moved around. 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 29, 2019, at 8:52 AM, Susan Lea <susan.lea@path.ox.ac.uk> wrote:
How can I generate a morph with a molecular surface representation?
many thanks Susan
Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Susan, You could add a command to color that patch of surface in your per-frame commands, right after creating the surface. E.g. alias stuff surf close; surf #3 & protein; color #3/A:25 orange target s perframe stuff; coordset #3 1,21; wait 21; ~perframe I would test the coloring command “manually” on one frame first, i.e. by typing into the command line to make sure it does what you want. In my example it colors the surface patch (coloring target s) orange for residue 25 in chain A of morph model #3. See color command <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> Maybe you didn’t color at every frame, only once. In that case the coloring would go away when you close the surface at each frame and create a new surface. I hope this helps, Elaine
On Apr 30, 2019, at 4:38 AM, Susan Lea <susan.lea@path.ox.ac.uk> wrote:
Dear Elaine,
this is great - nearly what I want! Now I'm getting fussy and want to color a residue on the surface but can't seem to get the colouring to stick.... any ideas?
thanks Susan
Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege
________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 29 April 2019 23:27:49 To: Susan Lea Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] morph with molecular surface for part of molecule
Hi Susan, Unfortunately it’s not as friendly as Chimera (yet). You would need to force recomputing the surface at each trajectory frame, for example with commands like the following for morph trajectory model #3:
alias stuff surf close; surf #3 & protein perframe stuff; coordset #3 1,21; wait 21; ~perframe
In that example I first create an alias “stuff” (could be some other word) that includes all the actions I want to do at each frame, then define it as a per-frame action to occur at each step of trajectory playback with the “coordset” command. The “wait” is required so that stopping the perframe action with “~perframe” won’t happen until after all the trajectory frames are played.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/wait.html>
Closing the surface is also required because otherwise “surface” thinks it doesn’t need to do anything because a surface for the same set of atoms is already there… it isn’t smart enough (yet) to realize that the atoms may have moved around. I hope this helps, Elaine
participants (2)
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Elaine Meng -
Susan Lea