How do you submit a sequence text file to BLAST/Modeller in ChimeraX?
Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
Hi Ralph, ChimeraX has the Modeller tools, which are totally separate from AlphaFold. ChimeraX menu: Tools... Structure Prediction... Modeller Comparative, and Model Loops. You can click Help on each tool dialog to see their documentation, or view copies at our website:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html
If you don't see these tools in your menu, you need to get a newer version of ChimeraX.
The documentation linked above describes how you could get an associated sequence or sequence alignment. Since you mentioned Blast I guess you want Modeller Comparative. In that page, it lists several ways you could get the alignment, including by opening a sequence alignment file or running the "blastprotein" command. I should update it to say you could also use the Blast Protein tool, menu: Tools... Sequence... Blast Protein, which is equivalent to using the command. After you run Blast there is a table listing the hits, and buttons across the bottom including "Show Sequence Alignment" which will open a sequence alignment of all of the hits you have chosen in the table. See Blast Protein help: https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results
So you would get the sequence alignment, make sure your template is associated with it, and show the Modeller Comparative tool, as described in the Modeller Comparative help. There is also a "modeller" command but it is easier to use the GUI tool, assuming you are not trying to script everything.
The documentation mentioned above is complete so you wouldn't necessarily benefit from a tutorial. I do have a loop-modeling tutorial https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html but that is different from the comparative modeling that I'm guessing you want to do.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2022, at 5:07 AM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, No, no, no! I know how to run Blast in ChimeraX if I have a PDB and use a sequence based on a selected chain. What I want to do, and was able to do in Chimera, is to start with just a sequence and no PDB and use Modeller to generate a PDB. I'd start out with Blast and there's a tab in Chimera BLAST labeled "Plain Text". I'd put my sequence into that, Blast against the PDB database, pick the best templates, show them in MAV and then go to Modeller to generate PDBs based on homology with the templates. How do I put a plain text sequence into the Blast tool in ChimeraX? There is no tab for that. And once I choose the best templates, how do I link those with Modeller? Are there any tutorials on this? I learned how to use Chimera/BLAST/Modeller using YouTube:
https://www.youtube.com/watch?v=6wSqI-iP_4w Ralph
On Wed, Nov 23, 2022 at 11:39 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ralph, ChimeraX has the Modeller tools, which are totally separate from AlphaFold. ChimeraX menu: Tools... Structure Prediction... Modeller Comparative, and Model Loops. You can click Help on each tool dialog to see their documentation, or view copies at our website:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html
If you don't see these tools in your menu, you need to get a newer version of ChimeraX.
The documentation linked above describes how you could get an associated sequence or sequence alignment. Since you mentioned Blast I guess you want Modeller Comparative. In that page, it lists several ways you could get the alignment, including by opening a sequence alignment file or running the "blastprotein" command. I should update it to say you could also use the Blast Protein tool, menu: Tools... Sequence... Blast Protein, which is equivalent to using the command. After you run Blast there is a table listing the hits, and buttons across the bottom including "Show Sequence Alignment" which will open a sequence alignment of all of the hits you have chosen in the table. See Blast Protein help: https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results
So you would get the sequence alignment, make sure your template is associated with it, and show the Modeller Comparative tool, as described in the Modeller Comparative help. There is also a "modeller" command but it is easier to use the GUI tool, assuming you are not trying to script everything.
The documentation mentioned above is complete so you wouldn't necessarily benefit from a tutorial. I do have a loop-modeling tutorial https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html but that is different from the comparative modeling that I'm guessing you want to do.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2022, at 5:07 AM, Ralph Loring via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Hi, When I was using Chimera and wanted to use Modeller, I would go to
sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks!
P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing
anything with this until after the holidays, so don't rush in answering.
Ralph Lorini
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Ralph, There is no plain text option for Blast, although there is a ticket requesting that improvement. https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5055
As I tried to convey, there is currently no tutorial for comparative modeling, but the steps are all given in the Modeller Comparative documentation:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html
(A) You can open the sequence from a file or fetch it from UniProt. There are links in that help page that give details on each of those. I.e. if you have just the sequence as text and it is not a UniProt entry, then you can use your favorite text-editor to make a FASTA file containing it, then open the FASTA file in ChimeraX so that it is shown in the Sequence Viewer. E.g. commands that show one sequence
open ~/Desktop/my-sequence-file.fa - or - open uniprot:ldlr_rat
(B) you can run Blast Protein with that sequence as the query, if your desired template structure isn't similar enough to associate with the target sequence. To do this you have to either use the Sequence Window's context menu: Tools... Blast Protein, or the command "blastprotein" https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context You show a context menu by right-clicking on the tool window (or if Mac trackpad or single-button mouse, Ctrl-clicking).
(C) It sounds like you already know how to show the multiple sequence alignment from Blast results in ChimeraX and to open the corresponding PDBs, so do that.
(D) start Modeller Comparative. The dialog will automatically have choices for the target sequence from the alignment. Choose which one is the target. All of the structures associated with the same alignment window in which the target sequence appears will be used as templates.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2022, at 12:00 PM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, No, no, no! I know how to run Blast in ChimeraX if I have a PDB and use a sequence based on a selected chain. What I want to do, and was able to do in Chimera, is to start with just a sequence and no PDB and use Modeller to generate a PDB. I'd start out with Blast and there's a tab in Chimera BLAST labeled "Plain Text". I'd put my sequence into that, Blast against the PDB database, pick the best templates, show them in MAV and then go to Modeller to generate PDBs based on homology with the templates. How do I put a plain text sequence into the Blast tool in ChimeraX? There is no tab for that. And once I choose the best templates, how do I link those with Modeller? Are there any tutorials on this? I learned how to use Chimera/BLAST/Modeller using YouTube: https://www.youtube.com/watch?v=6wSqI-iP_4w
Ralph
On Wed, Nov 23, 2022 at 11:39 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Ralph, ChimeraX has the Modeller tools, which are totally separate from AlphaFold. ChimeraX menu: Tools... Structure Prediction... Modeller Comparative, and Model Loops. You can click Help on each tool dialog to see their documentation, or view copies at our website:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html
If you don't see these tools in your menu, you need to get a newer version of ChimeraX.
The documentation linked above describes how you could get an associated sequence or sequence alignment. Since you mentioned Blast I guess you want Modeller Comparative. In that page, it lists several ways you could get the alignment, including by opening a sequence alignment file or running the "blastprotein" command. I should update it to say you could also use the Blast Protein tool, menu: Tools... Sequence... Blast Protein, which is equivalent to using the command. After you run Blast there is a table listing the hits, and buttons across the bottom including "Show Sequence Alignment" which will open a sequence alignment of all of the hits you have chosen in the table. See Blast Protein help: https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html#results
So you would get the sequence alignment, make sure your template is associated with it, and show the Modeller Comparative tool, as described in the Modeller Comparative help. There is also a "modeller" command but it is easier to use the GUI tool, assuming you are not trying to script everything.
The documentation mentioned above is complete so you wouldn't necessarily benefit from a tutorial. I do have a loop-modeling tutorial https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html but that is different from the comparative modeling that I'm guessing you want to do.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2022, at 5:07 AM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ 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 (2)
-
Elaine Meng -
Ralph Loring