Feature request: replace residues in model with residues from other model
Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias
Dear Eric, Thanks for opening the ticket. A related request regarding structural editing: I (and I suspect many others) often use ChimeraX to combine fragments of a chain from different models into a new model. For example, if model #1 contains residues 1-100 and residues 400-500 of chain A, and model #2 contains residues 200-300 in chain A, that I would use combine #1 #2 to generate a complete PDB. This will change the chain ID of what used to be chain A in model #2 to a new ID. Using changechains allows one to generate the compete chain A, however the resulting chain A is not correctly formatted in the PDB file. It will list residues 1-100, then reisdues 400-500, then residues 200-300, in that order. This destroys pseudobond display and also messes with certain sequence operations. It would be great if in such a case the resulting PDB file would be correctly formatted, so that residues appear in the the PDB file in the order of they sequence number. Many thanks, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Tuesday, 17. January 2023 at 22:40 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model Okay, I have opened an enhancement-request ticket in out bug-tracking database for this (https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323). It may take awhile before it gets implemented -- it is competing against quite a few other development priorities. --Eric On Jan 12, 2023, at 2:31 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : ) Many thanks, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:49 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that. If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement. --Eric On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would 1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another. I hope that made it clearer? Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Cc: "chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias _______________________________________________ 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 _______________________________________________ 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 _______________________________________________ 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
I *do* have some code squirreled away in ISOLDE to do essentially this, but it needs a little "hardening" before I expose it to the user interface. If you have an urgent need let me know and I'll take you through how to access it via ChimeraX's Python shell. Of course, if you're just talking about changes in coordinates and not actually changing the identities of any residues, then in ISOLDE you could just use the "source" model as a reference to set restraints on the target model and let a quick simulation do the rest. -- Tristan On Thu, Jan 12, 2023 at 5:49 PM Eric Pettersen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that.
If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.
--Eric
On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot, Matthias *From: *Eric Pettersen <pett@cgl.ucsf.edu> *Reply to: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Date: *Thursday, 12. January 2023 at 18:17 *To: *"Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> *Cc: *"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> *Subject: *Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance, Matthias _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Dear Tristan, Thanks a lot, that sounds great. I never considered using an ISOLDE simulation for that, that’s a cool idea. However, the coordinates wouldn’t end up being *exactly* the same as the reference model I assume? Very much looking forward for the code you mention, for now I can continue with my own workarounds but I think this will be a great addition making Isolde and ChimeraX even better for model building. Many thanks, Matthias From: Tristan Croll <tcroll@altoslabs.com> Date: Wednesday, 11. October 2023 at 14:33 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>, Eric Pettersen <pett@cgl.ucsf.edu> Cc: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model I do have some code squirreled away in ISOLDE to do essentially this, but it needs a little "hardening" before I expose it to the user interface. If you have an urgent need let me know and I'll take you through how to access it via ChimeraX's Python shell. Of course, if you're just talking about changes in coordinates and not actually changing the identities of any residues, then in ISOLDE you could just use the "source" model as a reference to set restraints on the target model and let a quick simulation do the rest. -- Tristan On Thu, Jan 12, 2023 at 5:49 PM Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that. If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement. --Eric On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would 1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another. I hope that made it clearer? Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Cc: "chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias _______________________________________________ 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 _______________________________________________ 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 _______________________________________________ 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 Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
That's correct - in general they wouldn't end up *exactly* the same - but you would get the advantage that the non-replaced atoms will also get the chance to shift to accommodate the changes. On Wed, Oct 11, 2023 at 1:37 PM Vorländer,Matthias Kopano < matthias.vorlaender@imp.ac.at> wrote:
Dear Tristan,
Thanks a lot, that sounds great. I never considered using an ISOLDE simulation for that, that’s a cool idea. However, the coordinates wouldn’t end up being **exactly** the same as the reference model I assume?
Very much looking forward for the code you mention, for now I can continue with my own workarounds but I think this will be a great addition making Isolde and ChimeraX even better for model building.
Many thanks,
Matthias
*From: *Tristan Croll <tcroll@altoslabs.com> *Date: *Wednesday, 11. October 2023 at 14:33 *To: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>, Eric Pettersen < pett@cgl.ucsf.edu> *Cc: *Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> *Subject: *Re: [chimerax-users] Feature request: replace residues in model with residues from other model
I *do* have some code squirreled away in ISOLDE to do essentially this, but it needs a little "hardening" before I expose it to the user interface. If you have an urgent need let me know and I'll take you through how to access it via ChimeraX's Python shell.
Of course, if you're just talking about changes in coordinates and not actually changing the identities of any residues, then in ISOLDE you could just use the "source" model as a reference to set restraints on the target model and let a quick simulation do the rest.
-- Tristan
On Thu, Jan 12, 2023 at 5:49 PM Eric Pettersen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that.
If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.
--Eric
On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot,
Matthias
*From: *Eric Pettersen <pett@cgl.ucsf.edu> *Reply to: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Date: *Thursday, 12. January 2023 at 18:17 *To: *"Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> *Cc: *"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> *Subject: *Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Hi Matthias,
I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way?
It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance,
Matthias
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Altos Labs UK Limited | England | Company reg 13484917
Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hi everyone, In the old Chimera, it was possible to assign a model ID to a file that was being opened. That was really helpful when writing scripts and made them more robust, because now if the order in which files are opened is changed, all downstream commands that use the model ID become messed up. Is this feature still somewhere hidden in ChimeraX, or, if not, could it be brought back? Other commands such as the the volume operations still have this feature (modelId in new-map-options…) Many thanks, Matthias
Hi Matthias, Currently "open" has a "name" (model name) option but not one to set the model ID number. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#models> I'll leave it to the others as to whether such an option will be added to "open", but currently you can change the model ID number in a subsequent step using the "rename" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I can understand it's not as convenient, however, since it requires knowing the original automatically assigned model number to specify the model you want to change. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2023, at 6:33 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone, In the old Chimera, it was possible to assign a model ID to a file that was being opened. That was really helpful when writing scripts and made them more robust, because now if the order in which files are opened is changed, all downstream commands that use the model ID become messed up. Is this feature still somewhere hidden in ChimeraX, or, if not, could it be brought back? Other commands such as the the volume operations still have this feature (modelId in new-map-options…) Many thanks, Matthias
Hi Matthias, In your example, to get the result you want do not use "changechains". Instead, form the C→N bond between residues 100 and 200 with "bond /A:100@C /[whatever]:200@N reasonable false". That will coalesce residues 200-300 into chain A and in the proper chain order. If desired, you could then delete the bond, which will leave behind a missing-structure pseudobond. --Eric
On Oct 11, 2023, at 1:44 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Eric,
Thanks for opening the ticket.
A related request regarding structural editing: I (and I suspect many others) often use ChimeraX to combine fragments of a chain from different models into a new model. For example, if model #1 contains residues 1-100 and residues 400-500 of chain A, and model #2 contains residues 200-300 in chain A, that I would use combine #1 #2 to generate a complete PDB. This will change the chain ID of what used to be chain A in model #2 to a new ID. Using changechains allows one to generate the compete chain A, however the resulting chain A is not correctly formatted in the PDB file. It will list residues 1-100, then reisdues 400-500, then residues 200-300, in that order. This destroys pseudobond display and also messes with certain sequence operations. It would be great if in such a case the resulting PDB file would be correctly formatted, so that residues appear in the the PDB file in the order of they sequence number.
Many thanks, Matthias
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Date: Tuesday, 17. January 2023 at 22:40 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Okay, I have opened an enhancement-request ticket in out bug-tracking database for this (https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323>). It may take awhile before it gets implemented -- it is competing against quite a few other development priorities.
--Eric
On Jan 12, 2023, at 2:31 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : ) Many thanks, Matthias
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:49 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that.
If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.
--Eric
On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
delete #1/A:1-10 select #2/A:1-10, save a pdb file with only the selected residues Open this new PDB file (model #3) combine #1,3 Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Cc: "chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance, Matthias _______________________________________________ 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>
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Hello, Not sure whether this already made it in to the backlog, but I'd vote for this as a useful feature, especially when scripting. Cheers, Alexis
Hello Alexis, I'm happy to report that this was added about a month ago! Builds from mid-Oct and later should have the "id" option to the "open" command, see <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#id> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 4:38 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, Not sure whether this already made it in to the backlog, but I'd vote for this as a useful feature, especially when scripting. Cheers, Alexis
Oooooh that's excellent. I guess I'll have to install the 1.7 rc. I had been waiting for ISOLDE, but I can keep two separate versions going for a while. Thanks Elaine & team!!! On Thu, Nov 16, 2023 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Alexis, I'm happy to report that this was added about a month ago! Builds from mid-Oct and later should have the "id" option to the "open" command, see
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#id>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 4:38 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, Not sure whether this already made it in to the backlog, but I'd vote for this as a useful feature, especially when scripting. Cheers, Alexis
Hi Alexis, Tristan released ISOLDE compatible with the ChimeraX 1.7 release candidates today. You can get it from ChimeraX menu Tools / More Tools. Tom
On Nov 16, 2023, at 4:44 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Oooooh that's excellent. I guess I'll have to install the 1.7 rc. I had been waiting for ISOLDE, but I can keep two separate versions going for a while.
Thanks Elaine & team!!!
On Thu, Nov 16, 2023 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hello Alexis, I'm happy to report that this was added about a month ago! Builds from mid-Oct and later should have the "id" option to the "open" command, see
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#id>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 4:38 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello, Not sure whether this already made it in to the backlog, but I'd vote for this as a useful feature, especially when scripting. Cheers, Alexis
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This day just keeps on getting better... :) On Thu, Nov 16, 2023 at 5:12 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
Tristan released ISOLDE compatible with the ChimeraX 1.7 release candidates today. You can get it from ChimeraX menu Tools / More Tools.
Tom
On Nov 16, 2023, at 4:44 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Oooooh that's excellent. I guess I'll have to install the 1.7 rc. I had been waiting for ISOLDE, but I can keep two separate versions going for a while.
Thanks Elaine & team!!!
On Thu, Nov 16, 2023 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Alexis, I'm happy to report that this was added about a month ago! Builds from mid-Oct and later should have the "id" option to the "open" command, see
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#id>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 4:38 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, Not sure whether this already made it in to the backlog, but I'd vote for this as a useful feature, especially when scripting. Cheers, Alexis
_______________________________________________ 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/
Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance, Matthias _______________________________________________ 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>
Hi Eric, Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would 1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another. I hope that made it clearer? Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias _______________________________________________ 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
So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that. If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement. --Eric
On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
delete #1/A:1-10 select #2/A:1-10, save a pdb file with only the selected residues Open this new PDB file (model #3) combine #1,3 Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> Cc: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance, Matthias _______________________________________________ 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>
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Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : ) Many thanks, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Date: Thursday, 12. January 2023 at 18:49 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that. If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement. --Eric On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Eric, Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would 1. delete #1/A:1-10 2. select #2/A:1-10, save a pdb file with only the selected residues 3. Open this new PDB file (model #3) 4. combine #1,3 5. Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 6. The I would use the command changechains #4/B A and this would yield the result that I want What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another. I hope that made it clearer? Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at<mailto:matthias.vorlaender@imp.ac.at>> Cc: "chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias _______________________________________________ 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 _______________________________________________ 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
Okay, I have opened an enhancement-request ticket in out bug-tracking database for this (https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323>). It may take awhile before it gets implemented -- it is competing against quite a few other development priorities. --Eric
On Jan 12, 2023, at 2:31 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : ) Many thanks, Matthias
From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:49 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This seems like something that the ISOLDE plugin would do already, but I'm not sure about that.
If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.
--Eric
On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Eric,
Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues 1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
delete #1/A:1-10 select #2/A:1-10, save a pdb file with only the selected residues Open this new PDB file (model #3) combine #1,3 Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4 The I would use the command changechains #4/B A and this would yield the result that I want
What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
I hope that made it clearer?
Thanks a lot, Matthias From: Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Reply to: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, 12. January 2023 at 18:17 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Cc: "chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [chimerax-users] Feature request: replace residues in model with residues from other model
Hi Matthias, I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you have to use the backbone conformation of the target. Are the side chain angles preserved in any way? It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX team,
Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.
Many thanks in advance, Matthias _______________________________________________ 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>
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participants (7)
-
a.rohou＠gmail.com -
Alexis Rohou
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Elaine Meng -
Eric Pettersen -
Tom Goddard -
Tristan Croll -
Vorländer,Matthias Kopano