Re: [Chimera-users] What is the default of ribbon?
Hi Root, You cannot change this preset, but you can control what is shown “manually," for example hiding all atoms and then displaying residues within 5 angstroms of ligand and 3.2 angstroms of ions with commands: ~disp disp ligand z<5 disp ions z<3.2 To make a more simple one-step action, you can make an “alias” combining several commands, and that could be listed in an Aliases menu. This is sort of like “make your own preset”. For examples, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007230.html> I hope this helps, Elaine On Aug 19, 2016, at 1:03 AM, 郭尚哲 <b02b02049@ntu.edu.tw> wrote:
Dear Elaine, I have another question. How can I change this 3.6 Å criteria, if it is possible? Root ________________________________________ 從: Elaine Meng [meng@cgl.ucsf.edu] 寄件日期: 2016年8月19日 上午 12:54 至: 郭尚哲 副本: chimera-users@cgl.ucsf.edu 主旨: Re: [Chimera-users] What is the default of ribbon?
Hi Root, It is described in the “preset” documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>
… specifically, "Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.”
In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms.
You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation. For example, you could search for “presets” or “ribbon interactive preset”. The information you found is explaining something different: why the backbone atoms are not shown.
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 Aug 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049@ntu.edu.tw> wrote:
Hi all, I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon... It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." I can't get more imformation, and still don't understand. What is the rule chimera follow to show the sidechain of certain residues? Thanks, Root
Dear Elaine, I tried it and was success. Thanks a lot! Root
Elaine Meng <meng@cgl.ucsf.edu> 於 2016年8月20日 00:10 寫道：
Hi Root, You cannot change this preset, but you can control what is shown “manually," for example hiding all atoms and then displaying residues within 5 angstroms of ligand and 3.2 angstroms of ions with commands:
~disp disp ligand z<5 disp ions z<3.2
To make a more simple one-step action, you can make an “alias” combining several commands, and that could be listed in an Aliases menu. This is sort of like “make your own preset”. For examples, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007230.html>
I hope this helps, Elaine
On Aug 19, 2016, at 1:03 AM, 郭尚哲 <b02b02049@ntu.edu.tw> wrote:
Dear Elaine, I have another question. How can I change this 3.6 Å criteria, if it is possible? Root ________________________________________ 從: Elaine Meng [meng@cgl.ucsf.edu] 寄件日期: 2016年8月19日 上午 12:54 至: 郭尚哲 副本: chimera-users@cgl.ucsf.edu 主旨: Re: [Chimera-users] What is the default of ribbon?
Hi Root, It is described in the “preset” documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>
… specifically, "Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.”
In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms.
You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation. For example, you could search for “presets” or “ribbon interactive preset”. The information you found is explaining something different: why the backbone atoms are not shown.
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 Aug 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049@ntu.edu.tw> wrote:
Hi all, I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbon... It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." I can't get more imformation, and still don't understand. What is the rule chimera follow to show the sidechain of certain residues? Thanks, Root
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