Hi All, I think there might be an easy way to do this, but haven't figured it out yet. I am interested in only selecting the waters on the surface of the protein, not those that are buried. Any suggestions? Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
Hi Wally, Here's one idea: while only the protein is included in the default (main) surface, you could use the command "surfcat" to lump the waters in with it. Then the surface waters should be the ones with nonzero surface area, or bigger than some small cutoff. Surface area per atom is an attribute, so you can use it in command-line specification, selection, etc. Detailed example (commands): open 2gbp surfcat blob protein | solvent surf blob ~surf When you create a molecular surface, the solvent-accessible and solvent-excluded areas per atom are automatically assigned as the atom attributes areaSAS and areaSES, respectively. There are also residue attributes by the same names. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
I undisplayed the surface after I made it so I could see the atoms, but the area values are still there. You could then select (or color, etc.) just the waters with area above some cutoff, for example: sel :hoh & :/areaSAS>20 - OR - (since areaSAS is the name of an atom attribute and residue attribute, which for only-O water is the same value) sel :hoh & @/areaSAS>20 - OR - sel @/areaSAS>20 ~sel protein First I tried using "solvent" instead of ":hoh" but that doesn't work, which made sense upon more thought: the "surfcat" command reassigned those atoms from the solvent surface category into the blob surface category, because surface categories are by definition mutually exclusive. Your waters might be named WAT instead of HOH, and of course you might want to use a different cutoff or areaSES instead of areaSAS. You can see a histogram of the area values in Render/Select by Attribute, and select interactively on the histogram with the Select part of that dialog, but be aware that would include the nonsolvent atoms as well. You would then have to ~sel protein, as in the last example above. I hope this helps! Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 21, 2008, at 9:02 AM, Walter Novak wrote:
Hi All, I think there might be an easy way to do this, but haven't figured it out yet. I am interested in only selecting the waters on the surface of the protein, not those that are buried. Any suggestions? Thanks, Wally
Hi Elaine, Thanks, this worked great!!! Best, Wally On Nov 21, 2008, at 12:48 PM, Elaine Meng wrote:
Hi Wally, Here's one idea: while only the protein is included in the default (main) surface, you could use the command "surfcat" to lump the waters in with it. Then the surface waters should be the ones with nonzero surface area, or bigger than some small cutoff. Surface area per atom is an attribute, so you can use it in command-line specification, selection, etc.
Detailed example (commands):
open 2gbp surfcat blob protein | solvent surf blob ~surf
When you create a molecular surface, the solvent-accessible and solvent-excluded areas per atom are automatically assigned as the atom attributes areaSAS and areaSES, respectively. There are also residue attributes by the same names. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
I undisplayed the surface after I made it so I could see the atoms, but the area values are still there. You could then select (or color, etc.) just the waters with area above some cutoff, for example:
sel :hoh & :/areaSAS>20
- OR - (since areaSAS is the name of an atom attribute and residue attribute, which for only-O water is the same value)
sel :hoh & @/areaSAS>20
- OR -
sel @/areaSAS>20 ~sel protein
First I tried using "solvent" instead of ":hoh" but that doesn't work, which made sense upon more thought: the "surfcat" command reassigned those atoms from the solvent surface category into the blob surface category, because surface categories are by definition mutually exclusive. Your waters might be named WAT instead of HOH, and of course you might want to use a different cutoff or areaSES instead of areaSAS.
You can see a histogram of the area values in Render/Select by Attribute, and select interactively on the histogram with the Select part of that dialog, but be aware that would include the nonsolvent atoms as well. You would then have to ~sel protein, as in the last example above.
I hope this helps! Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Nov 21, 2008, at 9:02 AM, Walter Novak wrote:
Hi All, I think there might be an easy way to do this, but haven't figured it out yet. I am interested in only selecting the waters on the surface of the protein, not those that are buried. Any suggestions? Thanks, Wally
Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
participants (2)
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Elaine Meng -
Walter Novak