Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD
Hello Edmund, No. However, there are probably dozens (hundreds?) of web services that will model proteins and write out PDB files that you can then open in any molecular graphics program. Within Chimera, besides the Modeller interface, you can "manually" build peptides of specified sequence and phi/psi angles and join them together (see Build Structure tool), or add amino acid residues one by one at the terminus ("addaa" command) or virtually mutate residues ("swapaa" command or Rotamers tool). Build Structure <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> Rotamers <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html> addaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html> swapaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.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 13, 2020, at 4:22 PM, Edmund Marinelli <edmundmarinelli@gmail.com> wrote:
Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD
Hello Elaine: So far I find no service that does what Modeller does, believe it or not. As an example Swiss-Model failed to fill in the missing residues, to my surprise. A couple of web services that I ran across rely on Modeller and one has to buy a license for Modeller or at least convince the Modeler lab that you are not commercial and qualify as academic, which is harder to do than one might think. There does exist the French server Pepfold3 and related versions but those don't handle the entire protein; instead one might get a 30-mer modeled 'on its own'. Then comes the question of : how would one mate that piece , which might have a different coordinate frame of reference , to the protein which lacks those residues in the PDB. This is a question, which on its own, is important. If you have any insight to that issue I would appreciate it. If you know of any service that actually models the protein and rebuilds the missing residues (note that the missing residues are listed in the PDB file , but of course no coordinates); I would be appreciative to know what they are. Best regards, Edmund R Marinelli (Ed) On Tue, Oct 13, 2020 at 4:52 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Edmund, No. However, there are probably dozens (hundreds?) of web services that will model proteins and write out PDB files that you can then open in any molecular graphics program.
Within Chimera, besides the Modeller interface, you can "manually" build peptides of specified sequence and phi/psi angles and join them together (see Build Structure tool), or add amino acid residues one by one at the terminus ("addaa" command) or virtually mutate residues ("swapaa" command or Rotamers tool).
Build Structure < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
Rotamers < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot....
addaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html> swapaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.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 13, 2020, at 4:22 PM, Edmund Marinelli <edmundmarinelli@gmail.com> wrote:
Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD
On 10/13/20 7:19 PM, Edmund Marinelli wrote:
A couple of web services that I ran across rely on Modeller and one has to buy a license for Modeller or at least convince the Modeler lab that you are not commercial and qualify as academic, which is harder to do than one might think.
I'm curious to know what problem you ran into. Assuming you actually are an academic, just fill out the license agreement at https://salilab.org/modeller/registration.html with details of your institution (we really don't take that much convincing). If you're not an academic, well sure, you're out of luck, sorry. Filling in missing residues is essentially just comparative modeling where the template is the PDB file without the residues and the target sequence has them added in (e.g. https://salilab.org/modeller/wiki/Missing%20residues), so I'm surprised to learn that other packages can't handle this. Ben -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
Dear Edmund, to my knowledge the SwissPDB Viewer, now Deep View, perform this task. When you open a pdb file lacking some residues it directly fills the gaps and gives a message that the build residues are in a different color (pink or purple, I guess). Best Marco Il 14/10/2020 04:19, Edmund Marinelli ha scritto:
Hello Elaine:
So far I find no service that does what Modeller does, believe it or not. As an example Swiss-Model failed to fill in the missing residues, to my surprise. A couple of web services that I ran across rely on Modeller and one has to buy a license for Modeller or at least convince the Modeler lab that you are not commercial and qualify as academic, which is harder to do than one might think. There does exist the French server Pepfold3 and related versions but those don't handle the entire protein; instead one might get a 30-mer modeled 'on its own'. Then comes the question of : how would one mate that piece , which might have a different coordinate frame of reference , to the protein which lacks those residues in the PDB. This is a question, which on its own, is important. If you have any insight to that issue I would appreciate it.
If you know of any service that actually models the protein and rebuilds the missing residues (note that the missing residues are listed in the PDB file , but of course no coordinates); I would be appreciative to know what they are.
Best regards,
Edmund R Marinelli (Ed)
On Tue, Oct 13, 2020 at 4:52 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hello Edmund, No. However, there are probably dozens (hundreds?) of web services that will model proteins and write out PDB files that you can then open in any molecular graphics program.
Within Chimera, besides the Modeller interface, you can "manually" build peptides of specified sequence and phi/psi angles and join them together (see Build Structure tool), or add amino acid residues one by one at the terminus ("addaa" command) or virtually mutate residues ("swapaa" command or Rotamers tool).
Build Structure <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> Rotamers <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html> addaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html> swapaa <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.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 13, 2020, at 4:22 PM, Edmund Marinelli <edmundmarinelli@gmail.com <mailto:edmundmarinelli@gmail.com>> wrote: > > Hello: > I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? > Thanks, > Edmund R Marinelli, PhD >
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participants (4)
-
Ben Webb -
Edmund Marinelli -
Elaine Meng -
Marco Sette