more questions about visualizing the backbone.
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out. I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand. How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms? I have included two peptide units that are hydrogen bonded to one another. Thanks Arthur G. Szabo
Hi Arthur, Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”. Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector. You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window. In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true. If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu: Actions… atoms/bonds… hide Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer) You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections. 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 Nov 28, 2016, at 4:02 PM, A G Szabo <agszabo@bell.net> wrote:
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out.
I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand.
How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms?
I have included two peptide units that are hydrogen bonded to one another. Thanks
Arthur G. Szabo
Elaine Thanks for your typically prompt reply. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-28-16 7:31 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] more questions about visualizing the backbone. Hi Arthur, Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”. Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector. You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window. In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true. If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu: Actions… atoms/bonds… hide Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer) You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections. 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 Nov 28, 2016, at 4:02 PM, A G Szabo <agszabo@bell.net> wrote:
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out.
I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand.
How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms?
I have included two peptide units that are hydrogen bonded to one another. Thanks
Arthur G. Szabo
Elaine A follow up question How can I color more than one atom, obviously the same color, at a time. Eg. The carbon atoms in tyrosine. I can select a single atom with ctrl-shift, how can I select all 6 atoms in the aromatic ring of tyrosine. Thanks Arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-28-16 7:31 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] more questions about visualizing the backbone. Hi Arthur, Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”. Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector. You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window. In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true. If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu: Actions… atoms/bonds… hide Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer) You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections. 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 Nov 28, 2016, at 4:02 PM, A G Szabo <agszabo@bell.net> wrote:
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out.
I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand.
How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms?
I have included two peptide units that are hydrogen bonded to one another. Thanks
Arthur G. Szabo
Elaine I figured out how to color all atoms the same color in the tyrosine ring. Used the command line. Thanks -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-28-16 7:31 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] more questions about visualizing the backbone. Hi Arthur, Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”. Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector. You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window. In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true. If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu: Actions… atoms/bonds… hide Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer) You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections. 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 Nov 28, 2016, at 4:02 PM, A G Szabo <agszabo@bell.net> wrote:
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out.
I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand.
How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms?
I have included two peptide units that are hydrogen bonded to one another. Thanks
Arthur G. Szabo
Elaine Sorry for asking so many what are likely trivial questions. When I visualize one chain from the whole model, I have figured out how to produce a nice ribbon backbone I can visualize all the atoms of the peptapeptide. I can hide the side chains leaving just the backbone atoms along with the ribbon I have generated. When all the atoms are visualized including the side chains and the backbone atoms, all the hydrogen atoms in the peptide, including the ones on the backbone nitrogen are shown. However, if I hide that side chains and visualize all atoms of the backbone, all the hydrogens on the backbone atoms disappear. Because I am trying to show the hydrogen bonding between adjacent chains in the extended beta sheet I would like to keep those hydrogens, but not the side chains. The latter just clutter the image. Comments? Thanks arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-28-16 7:31 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] more questions about visualizing the backbone. Hi Arthur, Chimera is using the secondary structure assignments as given in the input file (HELIX and SHEET lines in a PDB file), or if there were none, it tries to identify them by running “ksdssp”. Nevertheless you can manually reassign secondary structure however you like (even if it doesn’t make sense), for example by selecting residues and using the Selection Inspector. You can show that dialog with menu: Actions… Inspect or by clicking the green magnifying glass on the lower right corner of the Chimera window. In that dialog, Inspect: Residue and set (as needed) “in helix” to false and “in strand” to true. If all atoms of a residue or residues are selected, you can hide their sidechains but show their backbone atoms with menu: Actions… atoms/bonds… hide Actions… atoms/bonds… backbone only… full (or one of the other choices as you prefer) You can select all atoms of a residue or residues by selecting any atom or bond within them and then pressing keyboard up arrow to select the whole residue(s) containing those initial selections. 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 Nov 28, 2016, at 4:02 PM, A G Szabo <agszabo@bell.net> wrote:
Last week I asked a question regarding about how to visualize the backbone atoms. I have figured that out.
I am working with a peptide that forms an amyloid structure. The peptide strands form a beta sheet. When I select two of the peptide units that are hydrogen bonded to form two strands in the beta sheet, the strands are shown as a coil type structure rather than a flat beta strand.
How can I change the coil backbone to a beta strand structure? Second part is there a simple way to suppress the side chains but leaving the backbone atoms?
I have included two peptide units that are hydrogen bonded to one another. Thanks
Arthur G. Szabo
Hi Arthur, I guess our Actions menu menu “backbone” isn’t including the hydrogens. You could display backbone hydrogen atoms by their names using the command line. If you have proteins that use the standard atom names, then this should work: disp protein & @h,ha,h1,h2,h3,ha1,ha2,ha3 …or if you only want the ones on backbone nitrogens (not on the alpha-carbons): disp protein & @h,h1,h2,h3 For your other question, you are selecting or “picking” with the mouse on the structure, Ctrl-click selects one atom or bond and you can add to that selection with Shift-Ctrl-click, as desribed in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Pardon the delay, I was away from work yesterday. 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 Nov 29, 2016, at 11:26 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine Sorry for asking so many what are likely trivial questions.
When I visualize one chain from the whole model, I have figured out how to produce a nice ribbon backbone I can visualize all the atoms of the peptapeptide. I can hide the side chains leaving just the backbone atoms along with the ribbon I have generated. When all the atoms are visualized including the side chains and the backbone atoms, all the hydrogen atoms in the peptide, including the ones on the backbone nitrogen are shown. However, if I hide that side chains and visualize all atoms of the backbone, all the hydrogens on the backbone atoms disappear.
Because I am trying to show the hydrogen bonding between adjacent chains in the extended beta sheet I would like to keep those hydrogens, but not the side chains. The latter just clutter the image.
Comments? Thanks arthur
Elaine Thank you very much that is very helpful. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-30-16 12:37 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] more questions about visualizing the backbone. Hi Arthur, I guess our Actions menu menu “backbone” isn’t including the hydrogens. You could display backbone hydrogen atoms by their names using the command line. If you have proteins that use the standard atom names, then this should work: disp protein & @h,ha,h1,h2,h3,ha1,ha2,ha3 …or if you only want the ones on backbone nitrogens (not on the alpha-carbons): disp protein & @h,h1,h2,h3 For your other question, you are selecting or “picking” with the mouse on the structure, Ctrl-click selects one atom or bond and you can add to that selection with Shift-Ctrl-click, as desribed in: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Pardon the delay, I was away from work yesterday. 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 Nov 29, 2016, at 11:26 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine Sorry for asking so many what are likely trivial questions.
When I visualize one chain from the whole model, I have figured out how to produce a nice ribbon backbone I can visualize all the atoms of the peptapeptide. I can hide the side chains leaving just the backbone atoms along with the ribbon I have generated. When all the atoms are visualized including the side chains and the backbone atoms, all the hydrogen atoms in the peptide, including the ones on the backbone nitrogen are shown. However, if I hide that side chains and visualize all atoms of the backbone, all the hydrogens on the backbone atoms disappear.
Because I am trying to show the hydrogen bonding between adjacent chains in the extended beta sheet I would like to keep those hydrogens, but not the side chains. The latter just clutter the image.
Comments? Thanks arthur
participants (2)
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A G Szabo -
Elaine Meng