What do you do for comparative modeling if the pdb is so new it's not in UniProt?
Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help,
Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
Hi Ralph, I should say first that this may not be the right tool for your task, since it will only model a single chain (single subunit). However, if that is not a problem for you, I think I can answer your question.
It doesn't matter if the template protein is in UniProt. If I understand correctly, you have already opened a sequence of your target (the chimeric protein), and now you are trying to add the sequence from your template(s) to make an alignment? In the Sequence window of that target sequence, choose "Edit... Add Sequence" and then use the "From Structure" tab. (I.e. you need to first open the structure of your template and then you can add its sequence to the existing ones in the alignment via that tab.) You can alternatively paste in sequences "From Text" but probably the other way is easier. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit
Another way is to just create the whole alignment in some other application (e.g. Jalview) and then save it in some sequence-alignment format that Chimera can read, then open it in Chimera. Sequence formats: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment
Presumably you already had to text-edit to make a fasta file or use some other application to create the sequence of your target in the first place.
There is some discussion of how to get inputs for comparative modelling in Chimera here: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches
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 30, 2021, at 8:59 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help,
Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks, This is helpful
On Fri, Apr 30, 2021 at 12:25 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ralph, I should say first that this may not be the right tool for your task, since it will only model a single chain (single subunit). However, if that is not a problem for you, I think I can answer your question.
It doesn't matter if the template protein is in UniProt. If I understand correctly, you have already opened a sequence of your target (the chimeric protein), and now you are trying to add the sequence from your template(s) to make an alignment? In the Sequence window of that target sequence, choose "Edit... Add Sequence" and then use the "From Structure" tab. (I.e. you need to first open the structure of your template and then you can add its sequence to the existing ones in the alignment via that tab.) You can alternatively paste in sequences "From Text" but probably the other way is easier. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
Another way is to just create the whole alignment in some other application (e.g. Jalview) and then save it in some sequence-alignment format that Chimera can read, then open it in Chimera. Sequence formats: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment
Presumably you already had to text-edit to make a fasta file or use some other application to create the sequence of your target in the first place.
There is some discussion of how to get inputs for comparative modelling in Chimera here: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
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 30, 2021, at 8:59 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm very new to Chimera and have been working through the tutorials,
including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.
Thanks for your help,
Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
Hi Elaine, I'm trying to model single subunits, so this is what I need. However, something strange is going on with the BLAST protein function. If I BLAST the sequence NP_000737.1 in RSCB PDB (www.rcsb.org), it shows the following recently added PDBs (among others): 7EKT and 7KOO for human alpha7 receptors. However, if I blast the same sequence in chimera BLAST protein, the closest match is 6PV7 Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine [Homo sapiens]. For some reason, Chimera BLAST protein is not finding the appropriate structures. I would like to be able to use these structures in modeller. Is it something I'm doing, or is there a glitch in Chimera? Ralph
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
On Fri, Apr 30, 2021 at 12:25 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ralph, I should say first that this may not be the right tool for your task, since it will only model a single chain (single subunit). However, if that is not a problem for you, I think I can answer your question.
It doesn't matter if the template protein is in UniProt. If I understand correctly, you have already opened a sequence of your target (the chimeric protein), and now you are trying to add the sequence from your template(s) to make an alignment? In the Sequence window of that target sequence, choose "Edit... Add Sequence" and then use the "From Structure" tab. (I.e. you need to first open the structure of your template and then you can add its sequence to the existing ones in the alignment via that tab.) You can alternatively paste in sequences "From Text" but probably the other way is easier. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
Another way is to just create the whole alignment in some other application (e.g. Jalview) and then save it in some sequence-alignment format that Chimera can read, then open it in Chimera. Sequence formats: < https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment
Presumably you already had to text-edit to make a fasta file or use some other application to create the sequence of your target in the first place.
There is some discussion of how to get inputs for comparative modelling in Chimera here: < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m...
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 30, 2021, at 8:59 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm very new to Chimera and have been working through the tutorials,
including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial.
Thanks for your help,
Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
Hi Ralph, The Blast web service uses a local (on our web server machine) copy of the blast-searchable PDB protein sequence database. Although it is updated weekly, it may take a while for newly added structures to get into that database.
However, you do not have to use Blast to get your alignment. First open your target sequence file (fasta or whatever) so that it is shown in the Chimera sequence viewer. Then open whatever new structure(s) you want to use as template(s): 7ekt and 7koo, I guess from your e-mail. Then in the sequence window menu, use Edit... Add Sequence and in that dialog choose to add "From Structure" and specify the first template to add to the alignment, then Edit... Add Sequence again, From Structure, and specify the next template to add to the alignment, etc. for whatever number of templates you have, one or more.
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#add
If you'd added two template sequences to your target sequence, then now you should have an alignment of 3 sequences. If you don't think they are aligned well enough, choose sequence window menu Edit... Realign and calculate a new alignment until you're happy with it.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 24, 2021, at 5:51 AM, Ralph Loring rhloring@gmail.com wrote:
Hi Elaine, I'm trying to model single subunits, so this is what I need. However, something strange is going on with the BLAST protein function. If I BLAST the sequence NP_000737.1 in RSCB PDB (www.rcsb.org), it shows the following recently added PDBs (among others): 7EKT and 7KOO for human alpha7 receptors. However, if I blast the same sequence in chimera BLAST protein, the closest match is 6PV7 Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine [Homo sapiens]. For some reason, Chimera BLAST protein is not finding the appropriate structures. I would like to be able to use these structures in modeller. Is it something I'm doing, or is there a glitch in Chimera? Ralph
If you search for the sequences the PDB Data Bank (RCSB) provides both the pdb file and the sequence in fasta format.
Best regards,
Marco
Il 30/04/2021 17:59, Ralph Loring ha scritto:
Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help,
Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu mailto:r.loring@northeastern.edu
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Also, if you open a structure from the PDB in Chimera, then you can just use the Chimera menu: Favorites... Sequence to show the sequence of any/all of its biopolymer chains.
Elaine
On Apr 30, 2021, at 9:27 AM, Marco Sette sette@uniroma2.it wrote:
If you search for the sequences the PDB Data Bank (RCSB) provides both the pdb file and the sequence in fasta format.
Best regards,
Marco
Il 30/04/2021 17:59, Ralph Loring ha scritto:
Hi, I'm very new to Chimera and have been working through the tutorials, including the Comparative Modeling Tutorial. However I'm stumped. I'm interested in modeling chimeric proteins that involve the following pdbs: PDB 7KOO, 7KOX and 7KOQ and I can't get the sequence in my chimera to align with the template structure in the pdbs. The problem is that the template pdbs only came out in April and are not yet included in UniProt. They are deposited in RSCB and EMDB, but these don't appear to be alignment options in Chimera. Do I need to appeal to UniProt, or is there an alternative way to make the association between the sequence and the structure? Any additional tutorials on using MAV would be helpful as there seem to be a lot of editing features that are not explored in your tutorial. Thanks for your help,
Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it
e-mail: m77it@yahoo.it
Tel.: +39-0672594424 Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
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participants (3)
-
Elaine Meng -
Marco Sette -
Ralph Loring