Making New Bonds between two molecules in ChimeraX
Dear ChimeraX Admins and Elaine,
Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html), but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”.
For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route.
Thank you for your help!
Many thanks, Steven Truong sdt45@cam.ac.ukmailto:sdt45@cam.ac.uk Cambridge University
Steven,
The `bond` command is available in the ChimeraX daily build. They've also added this capability to the 'Build Structure' tool in the daily build.
I can't speak to why you're getting an error in Chimera - maybe Chimera is still interpreting the input as two separate models? Based on your example command, one of the molecules (#0.1) is a child of the other (#0), which would technically be a separate model. I don't work with PDB files too often, but look out for MODEL/ENDMDL in your file. If those are present, they'll define separate models.
If you're bent on doing this in ChimeraX 1.1, my SEQCROW bundle has a bond editor tool (Tools -> Structure Editing -> Bond Editor). You just select the atoms you want bonded and click 'draw bonds between selected atoms'. With the bond command imminent, I didn't bother adding my own command. It just made sense to have that capability on that tool. The atoms will still need to be on the same model.
Depending on how much you're adding, you might also be able to use SEQCROW to attach monosaccharides to residues or each other as 'substituents'. SEQCROW cannot put an added substituent in its own residue (yet). I can imagine this limitation might make using SEQCROW for this pretty awkward. You'll also have to add your saccharides to the list of substituents SEQCROW knows about. The process for this would look something like:
1. open/build a saccharide 2. open Tools -> AaronTools -> Add to Personal Library 3. select everything except the OH of whatever is going to be linked to another residue 4. enter a name on the tool * ignore conformer stuff, it's only used by a different program 5. click 'add current selection to library'
To add this substituent to a SER residue, for example:
1. select the SER's H on the hydroxyl group 2. add the saccharide using the command: * run `substitute sel substituent <your saccharide's name> [other options]` 3. or using the tool (Tools -> Structure Editing -> Change Substituents * enter your saccharide substituent's name on the 'Change Substituents' tool * check/uncheck any other options * click 'substitute current selection'
Best,
Tony ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Steven Truong sdt45@cam.ac.uk Sent: Wednesday, March 24, 2021 11:55 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Making New Bonds between two molecules in ChimeraX
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Dear ChimeraX Admins and Elaine,
Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html), but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”.
For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route.
Thank you for your help!
Many thanks, Steven Truong sdt45@cam.ac.ukmailto:sdt45@cam.ac.uk Cambridge University
Hi Steven, Tony is right, you cannot add a bond between different models in Chimera or ChimeraX, except for Chimera's Join Models (part of Build Structure tool), which would also reposition the models relative to each other. You wouldn't want to use Join Models if you've already pre-positioned the coordinates, however, and ChimeraX does not have Join Models yet. ChimeraX daily builds have the "bond" command and parts of Build Structure GUI, including Adjust Bond; these were added in September 2020, after the 1.1 release.
The "molecules" message in the Reply Log is confusing, I agree, and should really say "models" or "atomic models" instead.
Chimera Build Structure: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
ChimeraX Build Structure https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html
So in agreement with Tony, I believe you need to modify your input PDB files so that the atoms you want to bond are all opened as the same model. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 24, 2021, at 11:44 PM, Anthony James Schaefer tony.schaefer@uga.edu wrote:
Steven,
The `bond` command is available in the ChimeraX daily build. They've also added this capability to the 'Build Structure' tool in the daily build.
I can't speak to why you're getting an error in Chimera - maybe Chimera is still interpreting the input as two separate models? Based on your example command, one of the molecules (#0.1) is a child of the other (#0), which would technically be a separate model. I don't work with PDB files too often, but look out for MODEL/ENDMDL in your file. If those are present, they'll define separate models.
If you're bent on doing this in ChimeraX 1.1, my SEQCROW bundle has a bond editor tool (Tools -> Structure Editing -> Bond Editor). You just select the atoms you want bonded and click 'draw bonds between selected atoms'. With the bond command imminent, I didn't bother adding my own command. It just made sense to have that capability on that tool. The atoms will still need to be on the same model.
Depending on how much you're adding, you might also be able to use SEQCROW to attach monosaccharides to residues or each other as 'substituents'. SEQCROW cannot put an added substituent in its own residue (yet). I can imagine this limitation might make using SEQCROW for this pretty awkward. You'll also have to add your saccharides to the list of substituents SEQCROW knows about. The process for this would look something like: • open/build a saccharide • open Tools -> AaronTools -> Add to Personal Library • select everything except the OH of whatever is going to be linked to another residue • enter a name on the tool • ignore conformer stuff, it's only used by a different program • click 'add current selection to library' To add this substituent to a SER residue, for example: • select the SER's H on the hydroxyl group • add the saccharide using the command: • run `substitute sel substituent <your saccharide's name> [other options]` • or using the tool (Tools -> Structure Editing -> Change Substituents • enter your saccharide substituent's name on the 'Change Substituents' tool • check/uncheck any other options • click 'substitute current selection' Best,
Tony From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Steven Truong sdt45@cam.ac.uk Sent: Wednesday, March 24, 2021 11:55 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Making New Bonds between two molecules in ChimeraX
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Dear ChimeraX Admins and Elaine,
Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html), but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”.
For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route.
Thank you for your help!
Many thanks, Steven Truong sdt45@cam.ac.uk Cambridge University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Anthony James Schaefer -
Elaine Meng -
Steven Truong