Hi I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html... <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html...>. Could you please help? Thanks Yaikhomba
Currently, I think the shell is your friend here. First, select the two sulfurs. Then, in the shell: from chimerax.atomic import selected_atoms sel=selected_atoms(session) m = sel.unique_structures[0] m.new_bond(*sel) - Tristan
On 7 Apr 2020, at 12:24, Mutum YAikhombA <mutum.yaikhomba@mrc-mbu.cam.ac.uk> wrote:
Hi
I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html....
Could you please help? Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yaikhomba, Tristan’s answer is the only way to go in ChimeraX right now. Adding bonds via a tool or command is among the missing features we just haven’t gotten to yet. Alternatively, you could open your structure in Chiimera, make the the bond, and write out a PDB you could then open in ChimeraX. If you are going to be adding more than one bond, you can make Tristan’s method a little easier to access by turning the Python code into a “preset”. You would save his code into a file, and then follow the instructions in Presets→Add A Preset… to turn it into a preset (probably named something like “New Bond”). To use it you would then select two atoms and choose the New Bond preset. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2020, at 8:30 AM, Tristan Croll <tic20@cam.ac.uk> wrote:
Currently, I think the shell is your friend here. First, select the two sulfurs. Then, in the shell:
from chimerax.atomic import selected_atoms sel=selected_atoms(session) m = sel.unique_structures[0] m.new_bond(*sel)
- Tristan
On 7 Apr 2020, at 12:24, Mutum YAikhombA <mutum.yaikhomba@mrc-mbu.cam.ac.uk <mailto:mutum.yaikhomba@mrc-mbu.cam.ac.uk>> wrote:
Hi
I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html... <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html...>.
Could you please help? Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Yaikhomba, One more hacky way to add a bond, the "marker link" command. The marker command is intended to place markers on density maps and link them to trace paths. But it really just makes atoms and bonds. So to make your disulphide bond between residues 3 and 16: marker link :3,16@SG radius 0.2 This makes bond color yellow instead of matching the atoms, to remedy that: color :3,16@SG halfbond true You could make an alias to do these two commands alias bond marker link $1 radius 0.2 ; color $1 halfbond true then just use bond :3,16@SG Tom
On Apr 7, 2020, at 4:24 AM, Mutum YAikhombA <mutum.yaikhomba@mrc-mbu.cam.ac.uk> wrote:
Hi
I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html... <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html...>.
Could you please help? Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi guys, Let me try some of them and get back to you if they don’t work. Many thanks for the quick response! Yaikhomba
On 7 Apr 2020, at 18:14, Tom Goddard <goddard@sonic.net> wrote:
Hi Yaikhomba,
One more hacky way to add a bond, the "marker link" command. The marker command is intended to place markers on density maps and link them to trace paths. But it really just makes atoms and bonds. So to make your disulphide bond between residues 3 and 16:
marker link :3,16@SG radius 0.2
This makes bond color yellow instead of matching the atoms, to remedy that:
color :3,16@SG halfbond true
You could make an alias to do these two commands
alias bond marker link $1 radius 0.2 ; color $1 halfbond true
then just use
bond :3,16@SG
Tom
On Apr 7, 2020, at 4:24 AM, Mutum YAikhombA <mutum.yaikhomba@mrc-mbu.cam.ac.uk <mailto:mutum.yaikhomba@mrc-mbu.cam.ac.uk>> wrote:
Hi
I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX. I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html... <https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html...>.
Could you please help? Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
-
Eric Pettersen -
Mutum YAikhombA -
Mutum Yaikhomba
-
Tom Goddard -
Tristan Croll