Re: [Chimera-users] question
Hi Folks: I am having difficulty in converting C-terminal carboxyl to C-terminal amide on a beta sheet of 16 amino acids in length. When I try to get the complete amino acids displayed, it doesn't work. It just displays the main peptide cylinder. Thanks for your help. Jesse Jaynes On Thu, Oct 6, 2016 at 6:11 PM, Jaynes, Jesse <jjaynes@mytu.tuskegee.edu> wrote:
Hi Folks:
I am interested in generating a 23 amino acid peptide with several ornithines present. Is it possible? If not can I construct it with glutamine as a replacement for ornithine and then just take the carbonyl group and replace the oxygen with 2 hydrogens.
I just renewed my registration.
Thank You, Jesse Jaynes
On Thu, Oct 6, 2016 at 3:22 PM, Jaynes, Jesse <jjaynes@mytu.tuskegee.edu> wrote:
Hi Folks:
I am interested in generating a 23 amino acid peptide with several ornithines present. Is it possible? If not can I construct it with glutamine as a replacement for ornithine and then just take the carbonyl group and replace the oxygen with 2 hydrogens.
Thank You, Jesse Jaynes
Hi Jesse, My guess is that you are displaying ribbon, which automatically hides the backbone atoms. You can hide ribbon, for example with command “~ribbon” (or use Actions menu), or alternatively if you want to show both ribbon and backbone atoms at the same time, use command “ribbackbone”. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbon.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Best, 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 Oct 11, 2016, at 3:13 PM, Jaynes, Jesse <jjaynes@mytu.tuskegee.edu> wrote:
Hi Folks: I am having difficulty in converting C-terminal carboxyl to C-terminal amide on a beta sheet of 16 amino acids in length. When I try to get the complete amino acids displayed, it doesn't work. It just displays the main peptide cylinder. Thanks for your help. Jesse Jaynes
Hi Elaine: Thank you so much! You have been extremely helpful. I also was wondering how I might attach a fullerene with a peptide? I was going to do it through a sulfhydryl and an amino on the fullerene. Any ideas about how to do that? Thank you, Jesse On Tue, Oct 11, 2016 at 6:08 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jesse, My guess is that you are displaying ribbon, which automatically hides the backbone atoms. You can hide ribbon, for example with command “~ribbon” (or use Actions menu), or alternatively if you want to show both ribbon and backbone atoms at the same time, use command “ribbackbone”.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbon.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
Best, 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 Oct 11, 2016, at 3:13 PM, Jaynes, Jesse <jjaynes@mytu.tuskegee.edu> wrote:
Hi Folks: I am having difficulty in converting C-terminal carboxyl to C-terminal amide on a beta sheet of 16 amino acids in length. When I try to get the complete amino acids displayed, it doesn't work. It just displays the main peptide cylinder. Thanks for your help. Jesse Jaynes
Hi Jesse, Well, you’d have to work out what structure you want in terms of the chemistry. Then you could do some combination of changing atom types and building outwards gradually with the Modify Structure section of Build Structure, and opening “pieces” as separate models (for example, opening the fullerene structure separately) and then joining them together with the Join Models section of Build Structure. These tools take some practice getting used to, you would probably need to play around with them for a while. At least there is full documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> Not sure where you could get the fullerene 3D coordinates, if you don’t already have them. I saw there were fullerenes in PubChem, but when I tried pubchem fetch in Chimera, their 3D structures (at least the ones I tried) were not available using that method. Then I found this database with downloadable structures in “xyz” format but it was not the “xyz” format Chimera expected and could not be opened in Chimera: <http://www.nanotube.msu.edu/fullerene/fullerene-isomers.html> If you’re OK doing a little text-editing, you can fix this problem by simply removing the extra 4 columns of numbers at the ends of the atom lines in the xyz file from that database, and then open the xyz file in Chimera. Otherwise, you could use format-converting site to convert from xyz to pdb, and then open the resulting pdb in Chimera. <http://nl.webqc.org/molecularformatsconverter.php> … still somewhat laborious in that you have to paste in the contents of the xyz file (downloaded from that database, name ends in .xyz) and then copy and paste the output in a text-editor to create the pdb file (plain text file, name ends in .pdb), but not too bad if you’re only going to do it once or a few times. I hope this helps, 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 Oct 12, 2016, at 9:18 AM, Jaynes, Jesse <jjaynes@mytu.tuskegee.edu> wrote:
Hi Elaine: Thank you so much! You have been extremely helpful.
I also was wondering how I might attach a fullerene with a peptide? I was going to do it through a sulfhydryl and an amino on the fullerene. Any ideas about how to do that? Thank you, Jesse
participants (2)
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Elaine Meng -
Jaynes, Jesse