cavity cropped view
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest. Thanks, Randy
Hi Randy, You can use a "zone" specification, either with commands or via the menu. An example of the command approach: show ligand zr<5 or show :glc zr<5 The first example would show all residues [with any atom] within 5 angstroms of what is considered "ligand" ... in the second example, I gave a specific residue name. GLC is the residue name of glucose in the PDB entry 2gbp. You could also use a residue number or range of numbers. "za" instead of "zr" would just the atoms within the cutoff rather than their whole residues, and > instead of < gets the complementary set. The "show" command (unlike "display") undisplays everything that is not specified, so you don't have to undisplay anything beforehand. See the "Zones" section of http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html The mostly-menu approach has more steps: - select the small molecule (for example by Ctrl-clicking one of its atoms and then pressing the up arrow key) - use the command ~display to undisplay everything (if you use the Actions menu, it would just undisplay the current selection) - select a zone defined by the current selection (Select... Zone) with specified cutoff and whether you want it to be atom-based or residue-based - display that selection (for example, with Actions... Atoms/Bonds... show) I hope this helps, 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 Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest.
Thanks, Randy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Is it possible that doing this "zone" specification would only crop out the 'surf' repr if I had a decent graphics card? I *thought* I was able to do this on my work linux box w/ an nividia card, but am unable to do it on my wimpy Windows laptop or my wimpy Mac mini. -Randy
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 01, 2007 1:22 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] cavity cropped view
Hi Randy, You can use a "zone" specification, either with commands or via the menu. An example of the command approach:
show ligand zr<5 or show :glc zr<5
The first example would show all residues [with any atom] within 5 angstroms of what is considered "ligand" ... in the second example, I gave a specific residue name. GLC is the residue name of glucose in the PDB entry 2gbp. You could also use a residue number or range of numbers. "za" instead of "zr" would just the atoms within the cutoff rather than their whole residues, and > instead of < gets the complementary set. The "show" command (unlike "display") undisplays everything that is not specified, so you don't have to undisplay anything beforehand.
See the "Zones" section of http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html
The mostly-menu approach has more steps: - select the small molecule (for example by Ctrl-clicking one of its atoms and then pressing the up arrow key) - use the command ~display to undisplay everything (if you use the Actions menu, it would just undisplay the current selection) - select a zone defined by the current selection (Select... Zone) with specified cutoff and whether you want it to be atom-based or residue-based - display that selection (for example, with Actions... Atoms/Bonds... show)
I hope this helps, 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 Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest.
Thanks, Randy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Randy, This does not sound like a graphics hardware issue. All I can say is make sure you start with the surface hidden, and then just show surface for the zone. Displaying surface for a zone does not in itself hide the surface outside the zone. If you used a command, check that the command is typed correctly and that the atom specification really specifies what you wanted. You could alternatively accomplish the same task with the menu: hide all surface first, select the atoms used to define the zone, Select... Zone... and enter the desired cutoff, then show the surface for that zone. Best, 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 Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:
Is it possible that doing this "zone" specification would only crop out the 'surf' repr if I had a decent graphics card? I *thought* I was able to do this on my work linux box w/ an nividia card, but am unable to do it on my wimpy Windows laptop or my wimpy Mac mini.
-Randy
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 01, 2007 1:22 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] cavity cropped view
Hi Randy, You can use a "zone" specification, either with commands or via the menu. An example of the command approach:
show ligand zr<5 or show :glc zr<5
The first example would show all residues [with any atom] within 5 angstroms of what is considered "ligand" ... in the second example, I gave a specific residue name. GLC is the residue name of glucose in the PDB entry 2gbp. You could also use a residue number or range of numbers. "za" instead of "zr" would just the atoms within the cutoff rather than their whole residues, and > instead of < gets the complementary set. The "show" command (unlike "display") undisplays everything that is not specified, so you don't have to undisplay anything beforehand.
See the "Zones" section of http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html
The mostly-menu approach has more steps: - select the small molecule (for example by Ctrl-clicking one of its atoms and then pressing the up arrow key) - use the command ~display to undisplay everything (if you use the Actions menu, it would just undisplay the current selection) - select a zone defined by the current selection (Select... Zone) with specified cutoff and whether you want it to be atom-based or residue-based - display that selection (for example, with Actions... Atoms/Bonds... show)
I hope this helps, 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 Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest.
Thanks, Randy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
So does "unable to do it" mean that the command never finishes, or that it does finish but somehow doesn't produce the right result? --Eric On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:
Is it possible that doing this "zone" specification would only crop out the 'surf' repr if I had a decent graphics card? I *thought* I was able to do this on my work linux box w/ an nividia card, but am unable to do it on my wimpy Windows laptop or my wimpy Mac mini.
-Randy
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 01, 2007 1:22 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] cavity cropped view
Hi Randy, You can use a "zone" specification, either with commands or via the menu. An example of the command approach:
show ligand zr<5 or show :glc zr<5
The first example would show all residues [with any atom] within 5 angstroms of what is considered "ligand" ... in the second example, I gave a specific residue name. GLC is the residue name of glucose in the PDB entry 2gbp. You could also use a residue number or range of numbers. "za" instead of "zr" would just the atoms within the cutoff rather than their whole residues, and > instead of < gets the complementary set. The "show" command (unlike "display") undisplays everything that is not specified, so you don't have to undisplay anything beforehand.
See the "Zones" section of http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html
The mostly-menu approach has more steps: - select the small molecule (for example by Ctrl-clicking one of its atoms and then pressing the up arrow key) - use the command ~display to undisplay everything (if you use the Actions menu, it would just undisplay the current selection) - select a zone defined by the current selection (Select... Zone) with specified cutoff and whether you want it to be atom-based or residue-based - display that selection (for example, with Actions... Atoms/Bonds... show)
I hope this helps, 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 Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest.
Thanks, Randy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
The latter. I'm sure I'm simply doing something incorrect. BTW, I'm back on my Linux box and still can't get it work. I've tried to document what I'm attempting at: http://poincare.uits.iupui.edu/~heiland/chimera and hope someone can tell me what I'm doing wrong. Thanks, Randy
-----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Wednesday, February 14, 2007 4:20 PM To: Randy Heiland Cc: 'Elaine Meng'; chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] cavity cropped view
So does "unable to do it" mean that the command never finishes, or that it does finish but somehow doesn't produce the right result?
--Eric
On Feb 13, 2007, at 6:12 PM, Randy Heiland wrote:
Is it possible that doing this "zone" specification would only crop out the 'surf' repr if I had a decent graphics card? I *thought* I was able to do this on my work linux box w/ an nividia card, but am unable to do it on my wimpy Windows laptop or my wimpy Mac mini.
-Randy
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 01, 2007 1:22 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] cavity cropped view
Hi Randy, You can use a "zone" specification, either with commands or via the menu. An example of the command approach:
show ligand zr<5 or show :glc zr<5
The first example would show all residues [with any atom] within 5 angstroms of what is considered "ligand" ... in the second example, I gave a specific residue name. GLC is the residue name of glucose in the PDB entry 2gbp. You could also use a residue number or range of numbers. "za" instead of "zr" would just the atoms within the cutoff rather than their whole residues, and > instead of < gets the complementary set. The "show" command (unlike "display") undisplays everything that is not specified, so you don't have to undisplay anything beforehand.
See the "Zones" section of http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html
The mostly-menu approach has more steps: - select the small molecule (for example by Ctrl-clicking one of its atoms and then pressing the up arrow key) - use the command ~display to undisplay everything (if you use the Actions menu, it would just undisplay the current selection) - select a zone defined by the current selection (Select... Zone) with specified cutoff and whether you want it to be atom-based or residue-based - display that selection (for example, with Actions... Atoms/Bonds... show)
I hope this helps, 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 Feb 1, 2007, at 10:01 AM, Randy Heiland wrote:
What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest.
Thanks, Randy
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Randy, Here is the process you tried: # Here is what I attempted: display a protein (1yc1) # display a ligand (in purple) # 'surf' on the protein # select the ligand # '~display' --> removes the selected ligand # 'show sel zr<5' --> shows ligand + cropped stick repr of protein, but doesn't crop the surf The "show" command only acts on atoms/bonds (not ribbon, not surface ...). You have to use surf/~surf (or the menu) to show and hide surface. Here are two different approaches that will work. The first displays only the surface that you want. The second displays the whole surface and then undisplays the part outside the zone. command: open 1yc1 command: sel ligand zr<5 command: surf sel & main (the "& main" part says not to surface the ligand itself) -- OR -- command: open 1yc1 command: surf command: ~surf ligand zr>5 I hope this helps, 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 Feb 15, 2007, at 7:12 AM, Randy Heiland wrote:
The latter. I'm sure I'm simply doing something incorrect. BTW, I'm back on my Linux box and still can't get it work. I've tried to document what I'm attempting at: http://poincare.uits.iupui.edu/~heiland/chimera and hope someone can tell me what I'm doing wrong.
Thanks, Randy
Thanks very much, Elaine. Your 2nd approach did indeed produce the desired result for my case. (I should have mentioned that I was not using the 1yc1 protein from the PDB, which has a bound ligand, but rather was displaying 2 separate molecules from a local DB. Therefore I just substituted 'ligand' with 'sel' after I selected the ligand molecule). Aside: why doesn't the 'delete' cmd also delete the MSMS surface? It remains displayed, remains in the Model Panel, however I cannot graphically select it (in order to try to delete it).
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, February 15, 2007 11:58 AM To: Randy Heiland Cc: Chimera BB Subject: Re: [Chimera-users] cavity cropped view
Hi Randy, Here is the process you tried: # Here is what I attempted: display a protein (1yc1) # display a ligand (in purple) # 'surf' on the protein # select the ligand # '~display' --> removes the selected ligand # 'show sel zr<5' --> shows ligand + cropped stick repr of protein, but doesn't crop the surf
The "show" command only acts on atoms/bonds (not ribbon, not surface ...). You have to use surf/~surf (or the menu) to show and hide surface.
Here are two different approaches that will work. The first displays only the surface that you want. The second displays the whole surface and then undisplays the part outside the zone.
command: open 1yc1 command: sel ligand zr<5 command: surf sel & main
(the "& main" part says not to surface the ligand itself) -- OR --
command: open 1yc1 command: surf command: ~surf ligand zr>5
I hope this helps, 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 Feb 15, 2007, at 7:12 AM, Randy Heiland wrote:
The latter. I'm sure I'm simply doing something incorrect. BTW, I'm back on my Linux box and still can't get it work. I've tried to document what I'm attempting at: http://poincare.uits.iupui.edu/~heiland/chimera and hope someone can tell me what I'm doing wrong.
Thanks, Randy
Hi Randy, As defined, "delete" (like "show") is an operation on atoms/bonds, not the surface, which is a separate model. "~surf" can hide part or all of surfaces. You can get rid of a surface as a whole by choosing it in the left side of the Model Panel and clicking the "close" button on the right (not the Close button for the Model Panel!). I've described the current process rather than providing an answer to your question, which is more about design and data structures. We are planning changes to how surfaces are handled, including (I believe) allowing them to be selected, but I must leave it to the others who are/will be doing this work to provide any further details or the estimated time frame. I doubt there will be piecewise deletion as opposed to our current pattern of allowing partial hiding/ showing and deleting a surface as a whole. 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 Feb 15, 2007, at 9:25 AM, Randy Heiland wrote:
Aside: why doesn't the 'delete' cmd also delete the MSMS surface? It remains displayed, remains in the Model Panel, however I cannot graphically select it (in order to try to delete it).
participants (3)
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Elaine Meng -
Eric Pettersen -
Randy Heiland