Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
Dear Jay, I do not understand what you are trying to do. Superimpose what on what? If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues. The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer. If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
Dear Elaine, Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time. Sincerely, Jay On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Jay, I do not understand what you are trying to do. Superimpose what on what? If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues. The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer. If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
Hi Jay, When you open 6ir5, it already contains 4 copies of the monomer, chains A-D. I do not know which dimer you are trying to make, but maybe it's already there? See info page at RCSB, says global symmetry is cyclic - C2, and global stoichiometry is homo 4-mer <https://www.rcsb.org/structure/6IR5> From ChimeraX commands: open 6ir5 color bychain ... see attached screenshot ChimeraX window I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 10:37 PM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time. Sincerely, Jay
On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Jay, I do not understand what you are trying to do. Superimpose what on what?
If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues.
The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer.
If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, Thank you very much again for your kind reply and help. I want make a dimer of GII.3a and GII.3c (same protein) derived from homology modeling by Chimera onto chan A and C of 6ir5. In this step, I need to study more how to make it. If you have any advice, it would be much appreciated. I will take time to learn more. Thank you so much. Sincerely, Jay On Wednesday, August 4, 2021, 10:27:50 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Jay,When you open 6ir5, it already contains 4 copies of the monomer, chains A-D. I do not know which dimer you are trying to make, but maybe it's already there? See info page at RCSB, says global symmetry is cyclic - C2, and global stoichiometry is homo 4-mer<https://www.rcsb.org/structure/6IR5>
From ChimeraX commands: open 6ir5color bychain... see attached screenshot ChimeraX window I hope this helps,Elaine----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 10:37 PM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear Elaine, Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time. Sincerely, Jay On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Jay, I do not understand what you are trying to do. Superimpose what on what? If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues. The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer. If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Jay, Oh, you just want to put your GII.3a structure on top of 6ir5 chain A and your GII.3c structure on top of 6ir5 chain C. This is not too hard: First just open all three structures in ChimeraX. I opened 6ir5 first (model #1) and then your GII.3a structure (model #2) and then your GII.3c structure (model #3) and then used these commands matchmaker #2 to #1/A matchmaker #3 to #1/C See matchmaker help for details and other options like showing the sequence alignments: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> (Actually when I first opened the structures it looked like they were both already matched to chain A, but I included the chain A matching command above just in case.) ...then you can close #1 if you don't care about it any more: close #1 Then save one of those GII structures as a new PDB file, choosing the option to save it "relative to" the other one, so that later when you open the new saved PDB and the original of the other one, they will still form the dimer that you see on the screen. You can use menu: File... Save, or you can use the "save" command with "relModel" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> You can also (or instead) save the ChimeraX session with menu: FIle... Save or command "save" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2021, at 9:16 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, Thank you very much again for your kind reply and help. I want make a dimer of GII.3a and GII.3c (same protein) derived from homology modeling by Chimera onto chan A and C of 6ir5. In this step, I need to study more how to make it.
If you have any advice, it would be much appreciated. I will take time to learn more. Thank you so much. Sincerely, Jay
On Wednesday, August 4, 2021, 10:27:50 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jay, When you open 6ir5, it already contains 4 copies of the monomer, chains A-D. I do not know which dimer you are trying to make, but maybe it's already there?
See info page at RCSB, says global symmetry is cyclic - C2, and global stoichiometry is homo 4-mer <https://www.rcsb.org/structure/6IR5>
From ChimeraX commands:
open 6ir5 color bychain ... see attached screenshot ChimeraX window
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2021-08-04 at 8.25.05 AM.png>
On Aug 3, 2021, at 10:37 PM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time. Sincerely, Jay
On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Jay, I do not understand what you are trying to do. Superimpose what on what?
If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues.
The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer.
If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<aa TV24 6ir5 and 2CR28.fas><GII3 a.pdb><GII3 c.pdb><GII3 a c.tif><Screen Shot 2021-08-04 at 8.25.05 AM.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, Finally, I could make dimer of GII.3 novovirus according to your step-by-step advice . I am so thankful for your help so I can continue on writing my article paper. For my next papers I will never forget what you have taught me how to make multimers. Thank you very much for your time and help. This is really helpful!. Sincerely, Jay On Thursday, August 5, 2021, 01:35:02 AM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Jay, Oh, you just want to put your GII.3a structure on top of 6ir5 chain A and your GII.3c structure on top of 6ir5 chain C. This is not too hard: First just open all three structures in ChimeraX. I opened 6ir5 first (model #1) and then your GII.3a structure (model #2) and then your GII.3c structure (model #3) and then used these commands matchmaker #2 to #1/A matchmaker #3 to #1/C See matchmaker help for details and other options like showing the sequence alignments: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> (Actually when I first opened the structures it looked like they were both already matched to chain A, but I included the chain A matching command above just in case.) ...then you can close #1 if you don't care about it any more: close #1 Then save one of those GII structures as a new PDB file, choosing the option to save it "relative to" the other one, so that later when you open the new saved PDB and the original of the other one, they will still form the dimer that you see on the screen. You can use menu: File... Save, or you can use the "save" command with "relModel" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> You can also (or instead) save the ChimeraX session with menu: FIle... Save or command "save" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 4, 2021, at 9:16 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, Thank you very much again for your kind reply and help. I want make a dimer of GII.3a and GII.3c (same protein) derived from homology modeling by Chimera onto chan A and C of 6ir5. In this step, I need to study more how to make it.
If you have any advice, it would be much appreciated. I will take time to learn more. Thank you so much. Sincerely, Jay
On Wednesday, August 4, 2021, 10:27:50 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jay, When you open 6ir5, it already contains 4 copies of the monomer, chains A-D. I do not know which dimer you are trying to make, but maybe it's already there?
See info page at RCSB, says global symmetry is cyclic - C2, and global stoichiometry is homo 4-mer <https://www.rcsb.org/structure/6IR5>
From ChimeraX commands:
open 6ir5 color bychain ... see attached screenshot ChimeraX window
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2021-08-04 at 8.25.05 AM.png>
On Aug 3, 2021, at 10:37 PM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine, Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time. Sincerely, Jay
On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Jay, I do not understand what you are trying to do. Superimpose what on what?
If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do. You can still superimpose structures even if they are missing some residues.
The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1. I do not know what you did to get three submodels #2.1-3 for 3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer.
If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information. I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay
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<aa TV24 6ir5 and 2CR28.fas><GII3 a.pdb><GII3 c.pdb><GII3 a c.tif><Screen Shot 2021-08-04 at 8.25.05 AM.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
Wisoot Chanit