atoms/residues within a certain distance of another structure
Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry
On Mon, 2007-06-11 at 19:15 -0700, Terry Nelson wrote:
Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules", etc. I use a similar command in VMD that specifies the residues. 2. Does Chimera archive mails have a search engine that I missed? Cheers, Terry
Hi Terry, This can be done from the select menu or from the command line. For the menu approach, first select the species/residue(s) you are focused upon (say, the inhibitor mentioned above). Then, under Select, choose Zone... and finish off the details found in the window that appears (the choices are straighforward).
From the command line, use the "select" command, which has the format
select <description of atoms/residues> and add to the end of this one of the following: select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 The first (using z or zr) will pick up all residues less than 5.0 angstroms from the described atoms/residues, while the second gets only the atoms. You can use either greater than or less than. A more complete description of this can be found in the help files. Search for both "select" and "atom specification" for further information and specific examples. You may find it useful to start naming these selections if you plan to do more within each group. Check out "Name selection..." and (then) "Named selection" under the Select menu once you get the above working. HTH, Kenward -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???
On Jun 11, 2007, at 7:15 PM, Terry Nelson wrote:
Does Chimera archive mails have a search engine that I missed?
Hi Terry, You can search the chimera-users or chimera-dev archives from here: http://www.cgl.ucsf.edu/chimera/docs/feedback.html As Kenward mentioned, however, for how to do various things in Chimera it will usually be more fruitful to search the documentation (use Help... Search Documentation in the Chimera menu). This uses boolean combinations of terms and searches your local copy of the documentation, including the User's Guide, that came with the Chimera download. 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 Jun 12, 2007, at 12:25 AM, Kenward Vaughan wrote:
On Mon, 2007-06-11 at 19:15 -0700, Terry Nelson wrote:
Hi, 1. I was wondering if Chimera has the option of finding for instance : "residues within 5 Angstrom of a bound protein inhibitor" or "residues within 3Ang. of solvent molecules",
select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0
The only thing I would add is that Chimera guesstimates what parts of a system are ligand, solvent, etc., so "<description of atoms/ residues>" in the above may simply be "ligand" or "solvent". You can see what Chimera has classified as ligand/solvent with "select ligand" or "sel solvent". --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (4)
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Elaine Meng -
Eric Pettersen -
Kenward Vaughan -
Terry Nelson