Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions. francesco pietra
Hello Francesco, If you want to mutate a residue, you can try the swapaa command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html For instance: swapaa val #0:12.a lib Dunbrack preserve true where val is the target mutation, #0 gives the model number of the peptide in Chimera, 12.a says to make the mutation on residue position 12 of chain a, lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries to keep the rotamer of the mutation close to the original one. Hope this helps, Tim <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret@gmail.com>wrote:
Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions.
francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Francesco, Tim is totally right -- I just wanted to add that besides the "swapaa" command, there is also a graphical interface, the "Rotamers" tool, if you want to pick the sidechain conformation interactively. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 19, 2010, at 1:04 PM, Tim Travers wrote:
Hello Francesco,
If you want to mutate a residue, you can try the swapaa command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html
For instance: swapaa val #0:12.a lib Dunbrack preserve true
where val is the target mutation, #0 gives the model number of the peptide in Chimera, 12.a says to make the mutation on residue position 12 of chain a, lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries to keep the rotamer of the mutation close to the original one.
Hope this helps, Tim
On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret@gmail.com> wrote: Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions.
Thanks to Tim and Elaine. Tried successfully. However, I went to the Dunbrack web site noticing that in Dunbracks algorithm "Residues with names that do not match the standard 20 amino acid names are also treated as glycines" That is too bad for me as my peptide family is characterized by having a modified amino acid. Do you know of a software that accomplices the job with non-standard amino acids in the peptide? I used a molecular mechanics general program that may not the best solution and which does not read the (standard) pdb format of Chimera. It has its own pdb format which is read by VMD, not by Chimera. I also have a simulated annealing software that, however, is for vacuum. thanks francesco On Mon, Sep 20, 2010 at 5:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Tim is totally right -- I just wanted to add that besides the "swapaa" command, there is also a graphical interface, the "Rotamers" tool, if you want to pick the sidechain conformation interactively. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 19, 2010, at 1:04 PM, Tim Travers wrote:
Hello Francesco, If you want to mutate a residue, you can try the swapaa command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html For instance: swapaa val #0:12.a lib Dunbrack preserve true where val is the target mutation, #0 gives the model number of the peptide in Chimera, 12.a says to make the mutation on residue position 12 of chain a, lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries to keep the rotamer of the mutation close to the original one. Hope this helps, Tim On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret@gmail.com> wrote:
Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions.
Hi Francesco, Rotamer data comes from statistical analyses of structures in the PDB. Compared to standard amino acids, there is much less data for nonstandard amino acids, and I don't know of any program that provides or uses such data ("rotamer" information for nonstandard amino acids). As far as I know you would just have to build them manually, using Chimera or any of several other programs, and then do further molecular mechanics/dynamics calculations. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 26, 2010, at 8:46 AM, Francesco Pietra wrote:
Thanks to Tim and Elaine. Tried successfully. However, I went to the Dunbrack web site noticing that in Dunbracks algorithm
"Residues with names that do not match the standard 20 amino acid names are also treated as glycines"
That is too bad for me as my peptide family is characterized by having a modified amino acid. Do you know of a software that accomplices the job with non-standard amino acids in the peptide? I used a molecular mechanics general program that may not the best solution and which does not read the (standard) pdb format of Chimera. It has its own pdb format which is read by VMD, not by Chimera. I also have a simulated annealing software that, however, is for vacuum.
thanks
francesco
On Mon, Sep 20, 2010 at 5:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Tim is totally right -- I just wanted to add that besides the "swapaa" command, there is also a graphical interface, the "Rotamers" tool, if you want to pick the sidechain conformation interactively. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...
Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 19, 2010, at 1:04 PM, Tim Travers wrote:
Hello Francesco, If you want to mutate a residue, you can try the swapaa command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html For instance: swapaa val #0:12.a lib Dunbrack preserve true where val is the target mutation, #0 gives the model number of the peptide in Chimera, 12.a says to make the mutation on residue position 12 of chain a, lib Dunbrack tells to use the Dunbrack rotamer library, and preserve true tries to keep the rotamer of the mutation close to the original one. Hope this helps, Tim On Sun, Sep 19, 2010 at 1:43 PM, Francesco Pietra <chiendarret@gmail.com
wrote:
Hello: New to modify structure. I would like to modify a peptide by changing ARG to VAL. As I wanted to start from the conformer containing ARG, I tried to delete bonds, in the hope to finally change one H to CH3. None worked in my hands. Thanks for suggestions.
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participants (3)
-
Elaine Meng -
Francesco Pietra -
Tim Travers