Hi everyone, I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I've looked at the chimera manual and I am still confused on how these commands function. Thank you, Nikolay Rodionov
Hi Nikolay, The "atom specification" part of many commands (color, display, etc.) can include zones, for example: display :lys z<3 ... to display residues with any atom within 3 angstroms of lysine. Atom specification can be done in many ways ranging from simple to complex, so it is explained separately from the individual commands: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> See the "zones" section of that page. You can use za instead of z for atom-based rather than residue-based cutoff, and > instead of < for the complementary set. You can also combine specifications, for example: display solvent & :lys z<3 ... to display residues classified as solvent (could use :hoh instead) that have any atom within 3 angstroms of lysine. display solvent & :23.a z<3.5 ... solvent residues within 3.5 angstroms of residue 23 in chain A It is also possible to use the menus (see Select... Zone) but it would take more steps and commands are much better for complex specifications. 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 P.S. there are more atom-spec examples in the page linked above, as well as the Chimera Quick Reference (PDF) <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/quickref.pdf> On Apr 21, 2012, at 7:33 AM, Nikolay Igorovich Rodionov wrote:
Hi everyone,
I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I’ve looked at the chimera manual and I am still confused on how these commands function.
Thank you, Nikolay Rodionov
Just thought I should also mention that you'd probably want to undisplay all the water before doing the zone display: ~disp solvent - OR - ~disp :hoh Elaine
Hi Nikolay, ~disp solvent disp protein z<3 The word protein can be used to designate all the amino acids. Tom On Apr 21, 2012, at 9:54 AM, Elaine Meng wrote:
Hi Nikolay, The "atom specification" part of many commands (color, display, etc.) can include zones, for example:
display :lys z<3
... to display residues with any atom within 3 angstroms of lysine.
Atom specification can be done in many ways ranging from simple to complex, so it is explained separately from the individual commands:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
See the "zones" section of that page. You can use za instead of z for atom-based rather than residue-based cutoff, and > instead of < for the complementary set. You can also combine specifications, for example:
display solvent & :lys z<3
... to display residues classified as solvent (could use :hoh instead) that have any atom within 3 angstroms of lysine.
display solvent & :23.a z<3.5
... solvent residues within 3.5 angstroms of residue 23 in chain A
It is also possible to use the menus (see Select... Zone) but it would take more steps and commands are much better for complex specifications. 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
P.S. there are more atom-spec examples in the page linked above, as well as the Chimera Quick Reference (PDF) <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/quickref.pdf>
On Apr 21, 2012, at 7:33 AM, Nikolay Igorovich Rodionov wrote:
Hi everyone,
I am trying to display waters within a set distance from a solvated protein. Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I’ve looked at the chimera manual and I am still confused on how these commands function.
Thank you, Nikolay Rodionov
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participants (3)
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Elaine Meng -
Nikolay Igorovich Rodionov -
Tom Goddard