mmcif assemblies for alphafold prediction
Hello,
I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly?
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Hi Heather, I don't know what you mean by "similar to 4 and 6." The mmCIF information is for describing and applying symmetries, not making an asymmetric assembly.
Assuming that your ultimate goal is to generate such an assembly of your AlphaFold-predicted monomeric chain structures: If you have an assembly structure of some other similar proteins in that arrangement, you can open copies of your alphafold predictions and superimpose these copies onto the corresponding subunits of the known assembly (e.g. with "align" or "matchmaker" ... probably the latter, as it is easier if it works for your specific situation), then close that known assembly, leaving your approximately modeled assembly of AlphaFold models.
Matchmaker tool and command https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
align command https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Yes, so that is what I did. The "4 and 6" are the number of the assemblies I wanted to recreate which is the asymmetrical unit and crystal version of the unit. I did open up 1LP3 from the PDB bank super imposed to my alphfold prediction with matchmaker and then used the sym command for assembly #4 and #6. However, only the 1LP3 create the sym. The alphafold stays as a single superimposed monomer and I don't know why or how to fix it.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Fri, Oct 29, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Heather, I don't know what you mean by "similar to 4 and 6." The mmCIF information is for describing and applying symmetries, not making an asymmetric assembly.
Assuming that your ultimate goal is to generate such an assembly of your AlphaFold-predicted monomeric chain structures: If you have an assembly structure of some other similar proteins in that arrangement, you can open copies of your alphafold predictions and superimpose these copies onto the corresponding subunits of the known assembly (e.g. with "align" or "matchmaker" ... probably the latter, as it is easier if it works for your specific situation), then close that known assembly, leaving your approximately modeled assembly of AlphaFold models.
Matchmaker tool and command https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
align command https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with
an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly?
Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Hi Heather, You would not use "sym" for the alphafold model, only "matchmaker" ... what I described is that if you already have open a similar assembly of known structure, then open multiple copies of the alphafold model, then match each alphafold model copy onto one subunit of the other assembly.
It sounds like you are saying that the 1LP3 assembly is your known example. After you make the 1LP3 assembly with "sym", then open however many copies of the alphafold model would be in a similar assembly (i.e. open the same thing several times), then use "matchmaker" several times, once for each copy of the alphafold monomer, to superimpose it with the corresponding monomer of the 1LP3 assembly.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 30, 2021, at 4:35 AM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yes, so that is what I did. The "4 and 6" are the number of the assemblies I wanted to recreate which is the asymmetrical unit and crystal version of the unit. I did open up 1LP3 from the PDB bank super imposed to my alphfold prediction with matchmaker and then used the sym command for assembly #4 and #6. However, only the 1LP3 create the sym. The alphafold stays as a single superimposed monomer and I don't know why or how to fix it.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Fri, Oct 29, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, I don't know what you mean by "similar to 4 and 6." The mmCIF information is for describing and applying symmetries, not making an asymmetric assembly.
Assuming that your ultimate goal is to generate such an assembly of your AlphaFold-predicted monomeric chain structures: If you have an assembly structure of some other similar proteins in that arrangement, you can open copies of your alphafold predictions and superimpose these copies onto the corresponding subunits of the known assembly (e.g. with "align" or "matchmaker" ... probably the latter, as it is easier if it works for your specific situation), then close that known assembly, leaving your approximately modeled assembly of AlphaFold models.
Matchmaker tool and command https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
align command https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Ok, I see. I will try that thank you
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Sat, Oct 30, 2021, 10:17 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Heather, You would not use "sym" for the alphafold model, only "matchmaker" ... what I described is that if you already have open a similar assembly of known structure, then open multiple copies of the alphafold model, then match each alphafold model copy onto one subunit of the other assembly.
It sounds like you are saying that the 1LP3 assembly is your known example. After you make the 1LP3 assembly with "sym", then open however many copies of the alphafold model would be in a similar assembly (i.e. open the same thing several times), then use "matchmaker" several times, once for each copy of the alphafold monomer, to superimpose it with the corresponding monomer of the 1LP3 assembly.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 30, 2021, at 4:35 AM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Yes, so that is what I did. The "4 and 6" are the number of the
assemblies I wanted to recreate which is the asymmetrical unit and crystal version of the unit. I did open up 1LP3 from the PDB bank super imposed to my alphfold prediction with matchmaker and then used the sym command for assembly #4 and #6. However, only the 1LP3 create the sym. The alphafold stays as a single superimposed monomer and I don't know why or how to fix it.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Fri, Oct 29, 2021, 10:10 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Heather, I don't know what you mean by "similar to 4 and 6." The mmCIF
information is for describing and applying symmetries, not making an asymmetric assembly.
Assuming that your ultimate goal is to generate such an assembly of your
AlphaFold-predicted monomeric chain structures: If you have an assembly structure of some other similar proteins in that arrangement, you can open copies of your alphafold predictions and superimpose these copies onto the corresponding subunits of the known assembly (e.g. with "align" or "matchmaker" ... probably the latter, as it is easier if it works for your specific situation), then close that known assembly, leaving your approximately modeled assembly of AlphaFold models.
Matchmaker tool and command https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
align command https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with
an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly?
Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
participants (2)
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Elaine Meng -
Noriega, Heather