matchmaker question: restrict moving parts to selection?
Hi everyone,
Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false".
Example:
Mm #1:100-200 to #2/100-200 MoveWholeMolecule false
This should leave the residues 1-99 in model #1 unchanged.
I hope my question is clear. Thanks a lot in advance,
Matthias
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Hi Matthias, The "align" command has a similar option ("move atoms") but "matchmaker" does not, currently. To move that set of residues separately with matchmaker, you'd have to make it a separate model beforehand. Ways to do that:
(A) manually (by text-editing) create separate PDB files for the parts you want to move separately before opening them in ChimeraX (B) open the alphafold model multiple times and delete different parts from the different copies (C) use the "split" command with its "atoms" option, e.g.
split #1 atoms #1:100-200
https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html
Splitting would create two submodels, e.g. #1.1 with the specified atoms and #1.2 with the remainder. Check the Model Panel to see what the numbers are in your case, since it might be different. Then specify the desired submodel (or model, if you used methods A or B instead) in the matchmaker command, e.g.
mm #1.1 to #2:100-200
If you need all of the original #1 atoms in one model, you could then combine them back together:
combine #1.1-2 close true model #1
https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
Unfortunately that will use a new chain ID for those residues and there won't be peptide bonds between the different segments, so you'd still have to resort to manual editing to seamlessly incorporate those residues into their original chain.
We realize this is quite a rigamarole compared to a single option in the matchmaker command, so I'll make a ticket requesting it as a new feature. 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 15, 2022, at 10:22 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi everyone,
Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false".
Example:
Mm #1:100-200 to #2/100-200 MoveWholeMolecule false
This should leave the residues 1-99 in model #1 unchanged.
I hope my question is clear. Thanks a lot in advance,
Matthias
Dear Elaine,
Thanks a lot for your response and making a ticket! The problem with the "align" command is that it wonly works for selections with the same number of atoms (or am I doing something wrong?).
Looking forward to the new matchmaker feature in the future __ Best wishes, Matthias
On 15.04.22, 21:10, "Elaine Meng" meng@cgl.ucsf.edu wrote:
Hi Matthias, The "align" command has a similar option ("move atoms") but "matchmaker" does not, currently. To move that set of residues separately with matchmaker, you'd have to make it a separate model beforehand. Ways to do that:
(A) manually (by text-editing) create separate PDB files for the parts you want to move separately before opening them in ChimeraX (B) open the alphafold model multiple times and delete different parts from the different copies (C) use the "split" command with its "atoms" option, e.g.
split #1 atoms #1:100-200
https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html
Splitting would create two submodels, e.g. #1.1 with the specified atoms and #1.2 with the remainder. Check the Model Panel to see what the numbers are in your case, since it might be different. Then specify the desired submodel (or model, if you used methods A or B instead) in the matchmaker command, e.g.
mm #1.1 to #2:100-200
If you need all of the original #1 atoms in one model, you could then combine them back together:
combine #1.1-2 close true model #1
https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
Unfortunately that will use a new chain ID for those residues and there won't be peptide bonds between the different segments, so you'd still have to resort to manual editing to seamlessly incorporate those residues into their original chain.
We realize this is quite a rigamarole compared to a single option in the matchmaker command, so I'll make a ticket requesting it as a new feature. 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 15, 2022, at 10:22 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote: > > Hi everyone, > > Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false". > > Example: > > Mm #1:100-200 to #2/100-200 MoveWholeMolecule false > > This should leave the residues 1-99 in model #1 unchanged. > > I hope my question is clear. Thanks a lot in advance, > > Matthias
You are right, with "align" you need to specify the exact atoms to match between the two structures, and it has to be the same number from each. Matchmaker is easier because it uses sequence alignment to figure out the pairing for you; however, it only works for biopolymers and it only uses one atom per residue (alpha-carbons for proteins).
https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Best, Elaine
On Apr 17, 2022, at 11:13 PM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
Thanks a lot for your response and making a ticket! The problem with the "align" command is that it wonly works for selections with the same number of atoms (or am I doing something wrong?).
Looking forward to the new matchmaker feature in the future __ Best wishes, Matthias
On 15.04.22, 21:10, "Elaine Meng" meng@cgl.ucsf.edu wrote:
Hi Matthias, The "align" command has a similar option ("move atoms") but "matchmaker" does not, currently. To move that set of residues separately with matchmaker, you'd have to make it a separate model beforehand. Ways to do that:
(A) manually (by text-editing) create separate PDB files for the parts you want to move separately before opening them in ChimeraX (B) open the alphafold model multiple times and delete different parts from the different copies (C) use the "split" command with its "atoms" option, e.g.
split #1 atoms #1:100-200
https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html
Splitting would create two submodels, e.g. #1.1 with the specified atoms and #1.2 with the remainder. Check the Model Panel to see what the numbers are in your case, since it might be different. Then specify the desired submodel (or model, if you used methods A or B instead) in the matchmaker command, e.g.
mm #1.1 to #2:100-200
If you need all of the original #1 atoms in one model, you could then combine them back together:
combine #1.1-2 close true model #1
https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
Unfortunately that will use a new chain ID for those residues and there won't be peptide bonds between the different segments, so you'd still have to resort to manual editing to seamlessly incorporate those residues into their original chain.
We realize this is quite a rigamarole compared to a single option in the matchmaker command, so I'll make a ticket requesting it as a new feature. 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 15, 2022, at 10:22 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi everyone,
Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false".
Example:
Mm #1:100-200 to #2/100-200 MoveWholeMolecule false
This should leave the residues 1-99 in model #1 unchanged.
I hope my question is clear. Thanks a lot in advance,
Matthias
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
The align command has options "matchNumbering true", "matchAtomNames true", "matchChainIds true" that allow you to specify unequal numbers of atoms and it will only pair of the atoms that match. This is sometimes helpful for aligning slightly different structures.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html#pairing-opti... https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html#pairing-options
Tom
On Apr 18, 2022, at 8:52 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
You are right, with "align" you need to specify the exact atoms to match between the two structures, and it has to be the same number from each. Matchmaker is easier because it uses sequence alignment to figure out the pairing for you; however, it only works for biopolymers and it only uses one atom per residue (alpha-carbons for proteins).
https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
Best, Elaine
On Apr 17, 2022, at 11:13 PM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
Thanks a lot for your response and making a ticket! The problem with the "align" command is that it wonly works for selections with the same number of atoms (or am I doing something wrong?).
Looking forward to the new matchmaker feature in the future __ Best wishes, Matthias
On 15.04.22, 21:10, "Elaine Meng" meng@cgl.ucsf.edu wrote:
Hi Matthias, The "align" command has a similar option ("move atoms") but "matchmaker" does not, currently. To move that set of residues separately with matchmaker, you'd have to make it a separate model beforehand. Ways to do that:
(A) manually (by text-editing) create separate PDB files for the parts you want to move separately before opening them in ChimeraX (B) open the alphafold model multiple times and delete different parts from the different copies (C) use the "split" command with its "atoms" option, e.g.
split #1 atoms #1:100-200
https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html
Splitting would create two submodels, e.g. #1.1 with the specified atoms and #1.2 with the remainder. Check the Model Panel to see what the numbers are in your case, since it might be different. Then specify the desired submodel (or model, if you used methods A or B instead) in the matchmaker command, e.g.
mm #1.1 to #2:100-200
If you need all of the original #1 atoms in one model, you could then combine them back together:
combine #1.1-2 close true model #1
https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html
Unfortunately that will use a new chain ID for those residues and there won't be peptide bonds between the different segments, so you'd still have to resort to manual editing to seamlessly incorporate those residues into their original chain.
We realize this is quite a rigamarole compared to a single option in the matchmaker command, so I'll make a ticket requesting it as a new feature. 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 15, 2022, at 10:22 AM, Vorländer,Matthias Kopano via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi everyone,
Is it possible to align parts of a model to another while only moving the specified residues but not the rest of the molecule? A use case would be having an alphafold model from one species where the individual domains are correctly predicted, but don't agree with the relative orientation of the domains observed in a reference structure from another species. I envision this similar to the "fitmap" option "moveWholeMolecule false".
Example:
Mm #1:100-200 to #2/100-200 MoveWholeMolecule false
This should leave the residues 1-99 in model #1 unchanged.
I hope my question is clear. Thanks a lot in advance,
Matthias
ChimeraX-users mailing list 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 Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Tom Goddard -
Vorländer,Matthias Kopano